Manual Modules Loaded Module scripting commands General scripting commands Scripting

Modules currently available in Mesquite

MesquiteTrunk

• Mesquite Manual Information
  • This is the central module for the Mesquite system. In it is the main method that starts up the Mesquite application. This module loads information for all of the other modules, and hires FileCoordinator modules as needed to deal with open files. Thus, in the tree of employees that active modules make, this module is at its root.

CharacterSource

• Reshuffle Character Information
  • Supplies characters that are reshufflings of an existing character.
• Stored Characters Information
  • Supplies characters from data files (as opposed to simulated characters, for example).
• Calculated value for taxon Information
  • Supplies values for taxa reinterpreted as if characters.
• Simulated Characters on Trees Information
  • Supplies simulated characters each from a respective tree.
• Simulated Characters Information
  • Supplies simulated characters.
• ACGT Compositional Bias Information
  • Returns continuous characters which are the proportion G+C, and separately A, C, G, T, for each taxon in a DNA data set.
• Characters from Ordinations Information
  • Supplies a character from an ordination of an existing matrix.

CharsFromMatrixSource

• Characters from Matrix Source Information
  • Supplies characters from source of matrices.

CharacterModelSource

GenCodeModelSource

• Current Genetic Codes Information
  • Supplies the currently assigned genetic code (e.g., "standard") for a character.
• Stored Genetic Code Information
  • Supplies a user-specified genetic code, stored in the file.

ProbModelSourceSim

• Current Probability Model Set (for Simulation) Information
  • Supplies the currently assigned stochastic (likelihood, probability) model for a character for a simulation.
• Single Stored Probability Model for Simulation Information
  • Supplies a user-specified model of character evolution stored in the file for simulation.

ProbModelSourceLike

• Current probability models Information
  • Supplies the currently assigned stochastic (likelihood, probability) model for a character.
• Stored Probability Model Information
  • Supplies a user-specified model of character evolution stored in the file.

ParsModelSource

• Current Parsimony Models Information
  • Supplies the currently assigned parsimony model (e.g., "unordered") for a character.
• Stored Parsimony Model Information
  • Supplies a user-specified model of character evolution, for parsimony calculations, stored in the file. This can be different from the model assigned to the character as current in the List of Characters window.

TreeSource

• Default Trees Information
  • Supplies simple default trees (bush, ladder).
• Use Trees from Separate NEXUS File Information
  • Supplies trees directly from a file, without bringing the contained tree block entirely into memory. This is a special purpose module designed to allow much larger blocks of trees to be used within constraints of memory, but will make some calculations slower. Except for this special use, we recommend you use Include or Link from the file menu to access external tree files. This module does NOT copy the trees into your main data file, and so if you save your main data file then move it or the tree file, the data file will no longer be able to find the trees. This module does not know how many trees are in the file, and hence may attempt to read files beyond the number in the file.
• Sample Trees from Separate NEXUS File Information
  • Supplies a fixed number of randomly-sampled trees directly from a file, without bringing the contained tree block entirely into memory. This allows much larger blocks of trees to be used within constraints of memory, but will make some calculations slower. This module does not know how many trees are in the file, and hence may attempt to read files beyond the number in the file.
• Simulated Trees Information
  • Supplies trees from simulations.
• Stored Trees Information
  • Supplies trees stored, for instance in a file.
• Consensus Tree Information
  • Supplies consensus tree from a block of trees.
• MrBayes Max. A-Post. Tree Information
  • Supplies tree from MrBayes with highest posterior probability (MAP tree).
• MrBayes Trees from .t File Information
  • Supplies trees from a ".t" file produced by MrBayes
• All Trees Information
  • Supplies all possible dichotomous rooted or unrooted trees (only works if number of taxa is <=11).
• Concatenate Two Tree Sources Information
  • Concatenates two tree sources to yield a tree source first supplying trees from one source, then supplying trees from another. The trees are marked with values 1 and 2 to indicate the source.
• Concatenate Multiple Tree Sources Information
  • Concatenates multiple tree sources to yield a tree source supplying trees from each source. The trees are marked with values to indicate the source.
• Condensed Tree Source Information
  • Produces a block of trees that are a condensed version of another block of trees, with duplicate trees removed.
• Consensus Trees from Tree Blocks Information
  • Supplies consensus trees from Tree blocks.
• Current Tree Information
  • Supplies a single tree currently shown in a tree window.
• Modify Current Tree Information
  • Modifies current tree.
• Filter Trees from Other Source Information
  • Filters trees from another source.
• Transform Trees from Other Source Information
  • Transforms trees from another source.
• Randomly Modify Current Tree Information
  • Modifies current tree by random changes.
• Randomly Modify Trees Information
  • Modifies each of a series of trees by random changes; the i'th tree from this module comes by modifying the i'th tree from the original source of trees.

FileCoordinator

• Basic File Coordinator Information
  • Coordinates the reading, maintenance and linkages of files, which include Taxa, Trees, CharacterData, and other objects. This module is hired directly by the Mesquite trunk module.

FileInit

• File Comment Information
  • Manages the main file comment in a NEXUS file.
• Data Window Coordinator Information
  • Coordinates the creation of basic data windows.
• Manage Character Models Information
  • Manages character models.
• Save matrix copies Information
  • Provides for the saving of copies of matrices to separate files. This is available under the Characters menu.
• Initialize DNA Submodels Information
  • Initializes default DNA submodels.
• Initialize predefined categorical parsimony models Information
  • Initializes the predefined categorical parsimony models.
• Initialize predefined continuous parsimony models Information
  • Initializes the predefined continuous parsimony models.
• Initialize Parsimony Information
  • Initializes default character models for parsimony.
• Tree Window Coordinator Information
  • Coordinates the creation of basic tree windows.
• Export Matrices & Batch Files Information
  • Saves copies of matrices to separate files for subsequent batch analysis (e.g., parametric bootstrapping).
• Process File Information
  • Calls a File Processor to process the current file. Options depend on modules installed.
• Initialize predefined meristic parsimony models Information
  • Initializes the predefined meristic parsimony models.
• Initialize Genetic Code Information
  • Initializes default genetic codes.
• Manage Attached Notes Information
  • Manages (including NEXUS read/write) notes attached to taxa, characters and cells of matrices.
• Manage hyperlinks Information
  • Manages (including NEXUS read/write) hyperlinks.
• Manage pictures Information
  • Manages (including NEXUS read/write) pictures.

TemplateManager

• Batch File Template Manager Information
  • Manages templates used in saving batch files.

ManageCharModelsBlock

• Manage MESQUITECHARMODELS blocks Information
  • Manages MESQUITECHARMODELS block in NEXUS file.

ManageCodonsBlock

• Manage CODONS blocks Information
  • Manages CODONS block in NEXUS file.

ManageAssumptionsBlock

• Manage ASSUMPTIONS blocks Information
  • Manages ASSUMPTIONS block in NEXUS file.

ManageSetsBlock

• Manage SETS blocks Information
  • Manages character sets and other sets of various kinds (including read/write SETS block in NEXUS file).

ManageNotesBlock

• Manage NOTES blocks Information
  • Manages footnotes and pictures attached to taxa, characters and data points (including read/write NOTES block in NEXUS file).

ManageLabelsBlock

• Manage LABELS blocks Information
  • Manages LABELS block in NEXUS file.

ManageAuthors

• Manage AUTHORS blocks Information
  • Manages AUTHORS block in NEXUS file.

SpecsSetManager

• Manage Alternative Taxon Names Information
  • Manages (including NEXUS read/write) alternative taxon names.
• Manage taxa partititions Information
  • Manages (including NEXUS read/write) taxa partitions.
• Manage taxon sets Information
  • Manages (including NEXUS read/write) taxon sets.
• Manage character inclusion sets Information
  • Manages (including NEXUS read/write) character inclusion sets (EXSETS).
• Manage character partititions Information
  • Manages (including NEXUS read/write) character partitions.
• Manage character weight sets Information
  • Manages (including NEXUS read/write) character weight sets.
• Manage character sets Information
  • Manages (including NEXUS read/write) character sets (CHARSETS).
• Manage codon positions Information
  • Manages (including NEXUS read/write) codon position sets.
• Manage stored character orders Information
  • Manages (including NEXUS read/write) character orders.
• Manage parsimony model sets Information
  • Manages (including NEXUS read/write) parsimony model sets (TYPESETs).
• Manage probability model sets Information
  • Manages (including NEXUS read/write) probability model sets (PROBMODELSETs).
• Manage genetic code sets Information
  • Manages (including NEXUS read/write) genetic code sets (CODESETs).

FileInterpreter

FileInterpreterI

• Character/State Information Information
  • Exports character and state information for categorical matrix.
• Descriptions Information
  • Exports information in a matrix as a description.
• Fused Matrix Export (NEXUS) Information
  • Exports NEXUS files with matrices fused.
• Export NEXUS Tree File Information
  • Exports NEXUS file with a tree block, and optionally a taxa block.
• Export for PartitionFinder Information
  • Exports a .phy file containing your data prepared for PartitionFinder and creates a .cfg file.
• Export for PartitionFinderProtein Information
  • Exports a .phy file containing your data prepared for PartitionFinderProtein and creates a .cfg file.
• Export NEXUS Tree File from Tree Source Information
  • Exports NEXUS file with a tree block, and optionally a taxa block, based upon a source of trees. One major advantage of this is that it allows a collection of trees to a file without having them all in memory at once. For example, if the Tree Source is "Transform Trees From Other Source", and the other source is "Use Trees from Separate NEXUS file", then Mesquite will read in a tree from the other NEXUS file, transform the tree, and wrte it to the file, one at a tme.
• Clustal (DNA/RNA) Information
  • Imports Clustal files that consist of DNA or RNA sequence data.
• Clustal (protein) Information
  • Imports Clustal files that consist of amino acid sequence data.
• FASTA (DNA/RNA) Information
  • Imports and exports FASTA files that consist of DNA/RNA sequence data.
• FASTA (protein) Information
  • Imports and exports FASTA files that consist of amino acid sequence data.
• GenBank (DNA/RNA) Information
  • Imports GenBank files that consist of DNA/RNA sequence data.
• GenBank/GenPept (Protein) Information
  • Imports GenBank/GenPept files that consist of amino acid sequence data.
• Import Bayesian Consensus Tree File Information
  • Imports Bayesian Consensus Tree File (a NEXUS file) to capture metadata recorded at nodes
• NBRF/PIR (DNA/RNA) Information
  • Imports and exports NBRF files that consist of DNA/RNA sequence data.
• NBRF/PIR (protein) Information
  • Imports and exports NBRF files that consist of amino acid sequence data.
• POY (DNA/RNA) Information
  • Exports POY files of DNA/RNA sequence data.
• Simple (categorical data) Information
  • Imports and exports simple matrices that consist of basic categorical data. Exported data will consist of default symbols (0, 1, 2, ...).
• Simple (continuous data) Information
  • Imports and exports simple matrices that consist of basic continuous data.
• Simple (DNA/RNA) Information
  • Imports and exports simple matrices that consist of DNA/RNA sequence data.
• Simple (Geographic data) Information
  • Imports and exports simple matrices that consist of basic geographic data. The first character must be the latitude, and the second character the longitude.
• Simple (protein) Information
  • Imports and exports simple matrices that consist of amino acid sequence data.
• Tab-delimited categorical data file Information
  • Imports simple tab-delimited files of categorical data.
• Tab-delimited continuous data file Information
  • Imports and exports simple tab-delimited files of continuous data.
• Conservative NEXUS Information
  • Exports NEXUS files that avoid TITLE, LINK, IDS, the MESQUITE block, and other commands used mostly by Mesquite
• Export Partitions as Separate NEXUS files Information
  • Exports character partitions in a matrix as Separate NEXUS files.
• Simplified NEXUS Information
  • Exports NEXUS files, for instance of old fashioned style (using DATA block).
• NEXUS file Information
  • Coordinates the reading and writing of NEXUS files.
• Pagel format (ppy) file for Discrete Information
  • Imports and exports files formatted for Pagel's Discrete program.
• Pagel format (ppy) file for Multistate Information
  • Imports and exports files formatted for Pagel's Multistate program.
• Export Taxa Distance Matrix Information
  • Exports a tab-delimited text file of distances among the taxa.
• Export NEXUS for MrBayes Information
  • Exports NEXUS files for use by MrBayes.
• Export for OpenTree Information
  • Exports NEXUS file with a taxa and tree block for OpenTree based upon a source of trees.

FileInterpreterITree

• Fused Matrix Export (Phylip/RAxML) Information
  • Exports Phylip matrices that consist of multiple matrices, preparing them for RAxML.
• NONA, Hennig86, PiWe, WinClada Information
  • Imports and exports NONA/Hennig86/PiWe/WinClada files.
• Phylip (categorical data) Information
  • Imports and exports Phylip matrices that consist of basic categorical data with just two states. Exported data will consist of default symbols (0 and 1).
• Phylip (DNA/RNA) Information
  • Imports and exports Phylip matrices that consist of DNA/RNA sequence data.
• Phylip (protein) Information
  • Imports and exports Phylip matrices that consist of amino acid sequence data.
• Simple Newick/Phylip Treefile Information
  • Imports and exports Newick trees in the simple tree format used by Phylip and other programs.
• TNT Information
  • Imports and exports TNT files.

FileElementManager

AssociationsManager

• Manage TaxaAssociation blocks Information
  • Manages TaxaAssociation blocks in NEXUS file.

TreesManager

• Manage TREES blocks Information
  • Manages tree blocks (including read/write TREES block in NEXUS file).

TaxaManager

• Manage TAXA blocks Information
  • Manages sets of taxa (including read/write TAXA block in NEXUS file).

ScriptingManager

• Manage MESQUITE block Information
  • Manages MESQUITE block (including compose snapshot of current state of file in MESQUITE block "Auto" in NEXUS file).

CharactersManager

• Character Matrix manager Information
  • Coordinates the management of character data matrices.

ManagerAssistant

ListModule

• List of Character Group Labels Information
  • Makes windows listing character groups and information about them.
• List of Character Inclusion Sets Information
  • Makes windows listing character sets.
• List of Character Partitions Information
  • Makes windows listing character partitions.
• List of Character Sets Information
  • Makes windows listing character sets.
• Character List Information
  • Makes windows listing characters and information about them.
• List of Codon Positions Sets Information
  • Makes windows listing codon positions sets.
• Character Models List Information
  • Makes windows listing character models and information about them.
• List of Taxa Partitions Information
  • Makes windows listing taxa partitions.
• List of Taxon Group Labels Information
  • Makes windows listing taxon groups and information about them.
• Taxon List Information
  • Makes windows listing taxa and information about them.
• List of Taxon Sets Information
  • Makes windows listing taxon sets.
• List of Character Weight Sets Information
  • Makes windows listing character weight sets.
• List of Parsimony Model Sets Information
  • Makes a window listing parsimony model sets.
• List of Probability Model Sets Information
  • Makes windows listing probability model sets.
• List of Genetic Code Sets Information
  • Makes windows listing genetic code sets.

ListLVModule

• Character Matrices List Information
  • Makes windows listing character data matrices and information about them.
• NEXUS Blocks List Information
  • Makes windows listing NEXUS blocks.
• Taxa blocks list Information
  • Makes windows listing blocks of Taxa and information about them.
• Tree Blocks List Information
  • Makes windows listing tree blocks and information about them.
• Trees List Information
  • Makes windows listing trees and information about them.

FileAssistant

• Web page link Information
  • Provides a window to jump to a web page
• Go-to Window Information
  • Provides a window to jump to another file

FileAssistantM

• Merge Matrices from File Information
  • Includes a file and concatenates its taxa to an existing taxa block, for instance to add seqences.

FileAssistantT

• Multi Tree Window Information
  • Displays a special tree window with many trees simultaneously.
• Trees & Diversification Characters Information
  • Evolves a series of trees, each tied to a single character controlling diversification rates.
• Merge Taxa & Matrices from File Information
  • Includes a file and concatenates its taxa to an existing taxa block, for instance to add seqences.

FileAssistantCS

• Characters Scattergram Information
  • Makes a scatterplot displaying two values (such as likelihoods, parsimony scores, etc.) for a series of characters.
• Taxa Scattergram Information
  • Makes a scatterplot displaying two values (such as proportion of gaps in a sequence, etc.) for a series of taxa.
• Taxon Pairs Scattergram Information
  • Makes a chart comparing two values for each of many pairs of taxa.
• Trees Scattergram Information
  • Makes a scatterplot displaying two values (such as likelihoods, parsimony scores, imbalance statistics, correlations,etc.) for a series of trees.

FileAssistantCH

• Bar & Line Chart for Characters Information
  • Shows chart displaying values (such as likelihoods, parameter values, parsimony counts, etc.) for a series of characters.
• Bar & Line Chart for Character Matrices Information
  • Shows chart displaying values (such as treelength, etc.) for a series of character matrices.
• Taxon Pairs Histogram Information
  • Makes a chart showing some value for each of many pairs of taxa.
• Bar & Line Chart for Taxa Information
  • Makes a chart displaying values (such as proportion of gaps in a sequence, etc.) for each of a series of taxa.
• Tree Block Values Information
  • Makes a chart showing some value for each of many tree blocks.
• Bar & Line Chart for Trees Information
  • Makes a chart displaying values (such as likelihoods, parsimony scores, imbalance statistics, correlations,etc.) for a series of trees.

FileAssistantN

• Examples Navigator Information
  • Provides a Examples Navigator window with explanation and buttons to link to other files
• Text Window Information
  • Displays Text in a window.
• Picture Window Information
  • Displays a picture in a window.

FileAssistantA

• Summarize State Changes Over Trees Information
  • Summarizes reconstructions of state changes of a character over a series of trees.

BooleanForTree

• Selected Taxa Form Clade Information
  • Determines if the selected taxa form a clade in a tree.
• Selected Taxa Convex in Tree Information
  • Determines if the selected taxa are convex in a tree. That is, does there exist a rooting of the tree in which the selected taxa form a clade?
• Tree Congruent with Specified Tree Topology Information
  • Determines if tree matches topology of a specified tree. All trees must have the same taxa present.
• Tree Value Satisfies Criterion Information
  • Determines if the tree has a value either greater than, less than or equal to one specified.

NumberForTree

• Difference in steps in two characters Information
  • Calculates the difference between two characters in parsimony steps for a given tree.
• Steps in Character Information
  • Calculates the parsimony steps in a character for a given tree.
• Treelength Information
  • Calculates the parsimony length of a tree.
• Likelihood in Character Information
  • Calculates the negative log likelihood of a tree with respect to a single character.
• Boolean Tree Value Information
  • Gives a tree a value of 1 if it satisfies the criterion, 0 otherwise.
• Difference in two values for tree Information
  • Coordinates the calculation of the difference in two numbers for a tree.
• Attached Value Information
  • Supplies a number attached to the tree
• Value for Clade of Selected Taxa Information
  • Coordinates the calculation of a value for the clade of selected terminal taxa. If no terminal taxa are selected, the value at the root is given. If the selected taxa do not make a clade, no answer is returned.
• Value for Node Selected In Current Tree Information
  • Coordinates the calculation of a value for a node selected in a current tree. If no node or more than one node is selected in current tree, no result is returned. If the assessed tree does not share the same clade of the selected node, no answer is returned.
• Tree value using 2 characters Information
  • Coordinates the calculation of a number for a tree based on 2 characters.
• Number of Taxa Information
  • Counts the number of taxa in a tree.
• Ratio of Longest Branches Information
  • Gets the ratio of the two greatest branch lengths in a tree.
• Tree value using character matrix Information
  • Calculates a value for the tree using a character data matrix.
• Average Tree Depth Information
  • Calculates the average path length (in branch length) from terminals to the root, treating unassigned lengths as 0. The length of the root is not counted.
• Deep Coalescences Multiple Loci Information
  • Counts W. Maddison's (1997) number of extra gene lineages ("deep coalescences") for species tree containing a series of gene trees. The gene trees must be represented by a single taxa block.
• Deep Coalescences (gene tree) Information
  • Counts W. Maddison's (1997) number of extra gene lineages ("deep coalescences") for gene tree within species tree
• Deep Coalescences (species tree) Information
  • Counts W. Maddison's (1997) number of extra gene lineages ("deep coalescences") for species tree implied by a contained gene tree
• Gene Duplication-Extinction (gene tree) Information
  • Counts the number of duplication and extinction events for gene tree implied by a containing species tree
• Gene Duplication-Extinction (species tree) Information
  • Counts the number of duplication and extinction events for species tree implied by a contained gene tree
• s of Slatkin & Maddison Information
  • Calculates 's' of Slaktin & Maddison 1989 for tree of genes associated with given populations
• Tree Depth Information
  • Calculates the deepest path (in branch length) from terminals to the root, treating unassigned lengths as 0. The length of the root is not counted.
• MrBayes Score Information
  • Supplies posterior probability score from MrBayes
• Colless's Imbalance Information
  • Calculates Colless's Imbalance statistic for tree asymmetry, normalized by maximum asymmetry. Polytmous nodes are ignored in the calculation.
• Compare with Another Current Tree Information
  • Calculates a number relating a tree and another current tree (e.g., a tree-to-tree distance metric).
• Compare with Other Trees Information
  • Calculates a number relating one tree to another in a sequence (e.g., a tree-to-tree distance metric), such that the i'th tree is compared to the i'th other tree in the sequence.
• Number of SPR Rearrangements Information
  • Calculates the number of Subtree-Pruning-Regrafting branch rearrangements that can be done to a tree.
• Number of Congruent Trees Information
  • For the given tree, returns the number of trees in the tree source that are congruent with it.
• Sum of Branch Lengths Information
  • Calculates the sum of branch lengths of the tree, treating unassigned lengths as 0. The length of the root is counted.

NumberForTreeDivers

• Speciation/Extinction Likelihood Information
  • Calculates likelihoods using a speciation/extinction model reduced from the BiSSE model (Maddison, Midford & Otto 2007)

NumberForTreeM

• Tree value using character Information
  • Coordinates the calculation of a number for a tree based on a character.

NumberForCharacter

• Number of States Information
  • Shows the number of distinct states present in a categorical character
• Frequency of State Information
  • Calculates the frequency of a state for a categorical character
• Difference in two values for character Information
  • Coordinates the calculation of the difference in two numbers for a character.
• Number of Taxa with Non-Gap, Non-Missing Information
  • Calculates the number of taxa in the character that contain applicable, non-missing data.
• Character value using other character Information
  • Coordinates the calculation of a number for a character based on another character (e.g., a correlation between the two characters).
• Proportion Gaps In Character Information
  • Calculates the proportion of gaps (inapplicable codings) in a character across taxa. Does not include missing (unassigned) data.
• Proportion Missing Information
  • Calculates the proportion of missing data in a character across taxa.
• Value of item in taxon Information
  • Gives the value of an item for in a continuous character, for a specific taxon.
• Mean value of character Information
  • Calculates the mean observed trait for continuous character.
• Character value with current tree Information
  • Coordinates the calculation of a number for a character based on a current tree.
• Character value with tree Information
  • Coordinates the calculation of a number for a character based on a tree.
• Character Value with Respective Tree Information
  • Coordinates the calculation of a number for a character based on a respective tree.
• Character Compositional Bias Information
  • Calculates the percent of taxa with particular nucleotides (GC bias, or individual frequency of A, C, G or T) for a character.
• Mean value of character (linked matrix) Information
  • Calculates the mean observed trait for continuous character in a linked matrix.
• Proportion Polymorphic Information
  • Calculates the proportion of taxa coded as polymorphic or partially uncertain in a character.
• Proportion Internal Gaps Information
  • Calculates the proportion of internal gaps (inapplicable codings) in a character across taxa. Does not include missing (unassigned) data.
• Proportion Terminal Gaps Information
  • Calculates the proportion of Terminal gaps (inapplicable codings) in a character across taxa. Does not include missing (unassigned) data.
• Protein Site Property Information
  • Calculates the mean value of amino acid properties at a site across taxa.

CharacterLoadings

• Character Loadings Information
  • Returns loadings of a character in an ordination

NumberForCharAndTree

• Consistency Index for Character Information
  • Calculates the Consistency Index (CI) for a tree and character.
• Retention Index for Character Information
  • Calculates the Retention Index (RI) for a tree and character.
• Asymmetry Likelihood Ratio Test Information
  • Calculates the test statistic for the likelihood ratio test comparing the asymmetrical and one parameter models [2ln(L(Asymm.)/L(Mk1)], on a tree for a given character.
• Forward/Backward Rates Information
  • Uses maximum likelihood to estmate the rates of forward and backward changes (0 to 1 and 1 to 0 changes respectively), or alternatively the overall rate and the bias in gains versus losses, using the AsymmMk model on a tree for a given character.
• Mk1 Estimated Rate Information
  • Estimates the rate of a character's evolution under the simple Mk1 model.

NumForCharAndTreeDivers

• BiSSE Speciation/Extinction Likelihood Information
  • Calculates likelihood with a tree of a species diversification model whose speciation and extinction rates depend on the state of a binary character (BiSSE model, Maddison, Midford & Otto, 2007).
• BiSSE Ln Likelihood Difference Information
  • Calculates the difference in log likelihoods between two BiSSE speciation/extinction models.
• BiSSE Net Diversification Likelihood Information
  • Calculates likelihood with a tree of a species diversification model whose rates (r = spec. - ext.; a = spec./ext.) depend on the state of a binary character (BiSSE model, Maddison, Midford & Otto, 2007).
• Sister Diversification Information
  • Compares sister clades and returns the P value of the one-tailed null hypothesis that uniform clades of state 1 are smaller than uniform clades of state 0 among those with different values (P value calculated by Binomial probability).

CharacterLikelihood

• Character Likelihood Information
  • Calculates the negative log likelihood of a tree for a given character.

CharacterSteps

• Parsimony Character Steps Information
  • Calculates the number of parsimony steps in a character.

NumberForMatrix

• Fraction Applicable and Not Missing Information
  • Calculates the fraction of the matrix that is applicable and not missing data.
• Number of Characters Included Information
  • Calculates the number of characters in a matrix that are included.
• Number of Selected Taxa with Data in Matrix Information
  • Counts the number of taxa, among those selected, with data (not ? and not gaps) the matrix.
• Number of Taxa with Data in Matrix Information
  • Counts the number of taxa with data (not ? and not gaps) the matrix.
• Matrix value with current tree Information
  • Coordinates the calculation of a number for a character matrix based on a current tree.
• Pairwise Taxon Difference Information
  • Calculates distance between a specific pair of taxa based on a character matrix. Differs from Distance Between Taxa in thatit performs calculation for only a single pair of taxa.
• Average Sequence Length in Matrix Information
  • Calculates the average sequence length (non-gaps) in the matrix.
• Number of Internal Gaps in Matrix Information
  • Calculates the number of internal gaps in the matrix.
• Number of Stop Codons in Matrix Information
  • Calculates the number of stop codons in the matrix.

NumberForMatrixAndTree

• Consistency Index for Matrix Information
  • Calculates the Consistency Index (CI) for a tree and matrix.
• Retention Index for Matrix Information
  • Calculates the Retention Index (RI) for a tree and matrix.
• Treelength Information
  • Calculates the parsimony treelength of a given tree and matrix.

NumbersForNodes

• Number for Nodes from Attached Values Information
  • Supplies numbers for each node of a tree using values already attached to the nodes.
• Number for Nodes using Character Information
  • Supplies numbers, based on a character, for each node of a tree.
• Clade Match with Another Current Tree Information
  • Calculates a number relating each clade in the tree to another current tree (e.g., a tree-to-tree distance metric).
• Node Depth Information
  • Calculates the depth of each node from the highest terminal in its clade.
• Clade Frequencies in Trees Information
  • Calculates, for each clade in the tree, the frequency of that split among the trees in a specified tree source, or the frequency of the contradictory clade with the highest frequency, or the difference.

NumForNodesWithMat

• Number for Nodes using Matrix Information
  • Supplies numbers, based on a matrix, for each node of a tree.

NumbersForNodesIncr

• Map Continuous Information
  • Supplies a reconstruction of continuous-valued ancestral states on a tree. Differs from the basic reconstruction methods in that it supplies simply numbers for nodes, instead of a CharacterHistory

TreeWindowMaker

• Tree Window Information
  • Makes a basic tree window, which contains a tool palette. Hires assistants for the tree window (e.g., Trace Character).

TreeDisplayAssistant

TreeDisplayAssistantDI

• Color Branches by Partition Information
  • Colors the tree's branches by the taxon partition.
• Node or Branch-Associated Values Information
  • Shows values attached to nodes on the tree.
• Node or Branch-Associated Text Information
  • Shows text attached to nodes on the tree.

TreeDisplayAssistantD

• Label Branch Lengths Information
  • An assistant to a tree display that labels branches to show their lengths.
• Add Note On Tree Information
  • Draws editable notes in a tree display.
• Show Node Numbers Information
  • Shows the node numbers on a tree.

TreeDisplayAssistantI

• Branch Information Information
  • Provides a tool that shows information about branches.
• Branch Lengths Adjust Information
  • Provides a tool to adjust branch lengths of trees.
• Color Branches Information
  • Provides a tool with which to color branches in a tree window.
• Node Age Constraints Information
  • Supplies a tool for tree windows to set node age constraints. A short text string summarizes constraints. E.g. to say minimum age is 2.0, enter "2.0+". To say range is 2.0 to 4.0, enter "2.0-4.0". To say maximum is 4.0, enter "0.0-4.0". To say age is exactly 3.0, enter "3.0"
• Node Namer Information
  • Provides a tool to name the nodes of a tree
• Search within clade Information
  • Supplies a tool for tree windows that searches for a better branch arrangement within clade touched.
• Select Branches Information
  • Provides a tool and menu with which to select branches in a tree window.
• Select Taxa Information
  • Provides a tool with which to select taxa in a clade in a tree window.
• Insert Node Information
  • Provides a tool with which to insert nodes along a branch.
• Adjust scaling factor of lineage widths Information
  • Provides a tool with which to adjust the scaling factor used for lineage widths in a tree window.
• Annotate Branches Information
  • Supplies a tool for tree windows to attach and view footnotes for branches.
• Node Position Adjust Information
  • Provides a tool to adjust the depth of a node in the tree
• Projector Information
  • Supplies a projector tool for tree windows that allows pictures attached to taxa to be displayed.
• Taxon Link Information
  • Supplies a tool for tree windows that jumps to hypertext links for taxa.
• Get Taxon's tree from tolweb.org Information
  • Supplies a tool for tree windows that gets tree for taxon touched from tolweb.org
• Get Taxon's tree from a web site Information
  • Supplies a tool for tree windows that gets tree for taxon touched from a web site.
• Make Rerootings of Clade Information
  • Presents a tool by which you can touch on a tree; a tree block is made consisting of trees representing all rerootings of the clade of the node touched.
• Randomly Rotate Branches Information
  • Supplies a tool for tree windows that randomly rotates branches in clade touched.

TreeDisplayAssistantA

• Trace All Characters Information
  • Summarizes for each node the reconstructions of the states at all characters of the tree.
• Trace Character Over Trees Information
  • Summarizes at each node reconstructions of the states of a character over a series of trees. The summary is shown on the current tree; if you want to show it on a consensus of the trees, make sure that the current tree is that consensus.

TreeDisplayAssistantMA

• Trace Character History Information
  • Traces a history of character evolution on the nodes of a drawn tree.
• Values for Current Tree Information
  • Makes the legend in a tree window to display the tree name and values pertaining to the tree.
• Values for Nodes Information
  • Shows on a drawn tree various possible numbers at the nodes.
• Pairwise Comparison Information
  • Performs pairwise comparison character correlation tests. Phylogenetically independent pairs are chosen, and the states of two binary characters are compared to see if they are correlated among these pairs.
• Landmark Drawings Information
  • Places drawing of landmarks at each node in tree.

TreeWindowAssistant

TreeWindowAssistantA

• Correlation Analysis Information
  • Performs a Correlation analysis for categorical characters.
• Character-Associated Diversification Information
  • Coordinates analyses for the effect of a character on diversification (speciation/extinction).
• Diversification (Char. Indep.) Information
  • Coordinates analyses of diversification (speciation/extinction).
• Lineages Through Time Information
  • Displays a window showing plot of lineages through time averaged over many trees.

TreeWindowAssistantI

• Tree Utility Coordinator Information
  • Coordinates use of tree utilities in tree window

TreeWindowAssistantN

• Dependent Tree Window Information
  • Displays a single tree (the same as in a tree window).
• Mirror Tree Window Information
  • Displays a single tree (the same as in a tree window) twice, in mirror image.

TreeWindowAssistantC

• Nodes Scattergram Information
  • Shows values for nodes of tree via a scattergram.

TreeWindowAssistantOA

• Summarize Changes In Selected Clade Over Trees Information
  • Summarizes reconstructions of state changes of a character on descendants of selected branch, over a series of trees. The branches defined are those that are the descendants of the single branch selected on the tree in the tree window.
• Likelihood Surface AsymmMk Model Information
  • Shows the likelihood surface for the AsymmMk Model.

DrawTreeCoordinator

• Basic Tree Draw Coordinator Information
  • Coordinates the drawing of a tree by maintaining the basic TreeDisplay and by hiring a DrawTree module.

DrawTree

• Curvogram Information
  • Draws trees with curved branches (as PHYLIP's 'Curvogram').
• Balls & Sticks Information
  • Draws trees with spots and the nodes and thin lines for branches.
• Diagonal tree Information
  • Draws trees with standard diagonal branches ("cladogram")
• Square Line Tree Information
  • Draws trees with square branches made out of lines rather than polygons.
• Classic Square tree Information
  • Draws trees with standard square branches ("phenogram")
• Circular tree Information
  • Draws trees in circular form.
• Constellation Information
  • Draws trees with spots at the nodes in a more or less unrooted way.

AnalyticalDrawTree

• Plot Tree Information
  • Draws trees plotted in a two dimensional space.
• Contained Gene (or Other) Trees Information
  • Draws wide trees containing trees of associates (e.g., species tree containing gene tree)
• Plot Tree 3D Information
  • Draws trees plotted in a three dimensional space.

NodeLocs

NodeLocsPlot3D

• Node Locations (3D plot) Information
  • Calculates the node locations for a tree plotted in a three dimensional space.

NodeLocsUnrooted

• Node Locations (unrooted) Information
  • Calculates the node locations for a tree drawn in unrooted fashion.

NodeLocsFree

• Node Locations (oval) Information
  • Calculates the node locations for a tree drawn in oval fashion, with root at center.

NodeLocsCircle

• Node Locations (circle) Information
  • Calculates the node locations for a tree drawn in circular fashion, with root at center.

NodeLocsVH

• Node Locations (standard) Information
  • Calculates the node locations in a tree drawing, for use with vertical or horizontal tree drawers (e.g., the standard diagnonal or square trees).

NodeLocsPlot

• Node Locations (2D plot) Information
  • Calculates the node locations for a tree plotted in a two dimensional space.

DrawNamesTreeDisplay

• Basic Draw Names for Tree Display Information
  • Draws taxon names on a tree. Chooses orientation of names according to orientation of tree.

TaxaWindowMaker

TaxaDisplayAssistant

TaxaWindowAssistant

DrawTaxaCoordinator

DrawTaxa

DrawNamesTaxaDisplay

DataWindowMaker

• Character Matrix Editor Information
  • Makes editor windows to edit character data.

DataWindowAssistant

DataWindowAssistantA

• Show Distance Matrix Information
  • Writes distance matrix to log.

DataWSelectionAssistant

• Extend Selection to Whole Characters Information
  • Selects a character if a cell for that character is selected.
• Select by Matrix Comparison Information
  • Selects cells of the matrix that differ compared to another matrix
• Select Matching Taxa Information
  • Selects taxa according to whether their sequence of states matches the sequence of states in the selected taxon
• Select Same Subsequence Information
  • Selects cells of the matrix according to whether their sequence of states matches the sequence of states in the selected taxon or block of cells
• Select Same Distribution Information
  • Selects cells of the matrix according to whether their distribution of states across taxa in a character is the same as that in the selected character or block of cells
• Select Lowercase Ends Information
  • Selects ends of a DNA sequence up to the first block of N sites in a row with uppercase (confident) symbols (the user chooses N). Assuming that lowercase letters are used for less certain base calls, this can be used to select and then trim (by painting with gaps) poorly-sequenced terminal regions.

CategDataEditorInit

• Edit State Names Information
  • Edits state names of a categorical data matrix.

DataWindowAssistantI

• Add/Delete Data Information
  • Adds and deletes characters and taxa in a Character Matrix editor. This can be done through the Add characters..., Add taxa..., and Delete Selected menu items and via the tools that add taxa and characters where touched.
• Alter Data Information
  • Manages data-transforming modules.
• Data Painter Information
  • Supplies the paint can tool and dropper tool for filling cells in a character data editor.
• Matrix Info Information
  • Shows Information about the data in each taxon.
• Character matrix selection coordinator Information
  • Coordinates selecting taxa and characters in data matrix.
• Popup Menu State Entry Information
  • Provides a tool with which to quickly enter data by providing a popup menu of states.
• Quick Key Entry Information
  • Provides a tool with which to quickly enter data. If this tool is active, then typing a key will cause that value to be entered into all selected cells.
• Search Data Information
  • Manages data-searching modules.
• Select By Search (Find all) Information
  • Selects cells of the matrix according to whether their text contains a given string
• Character Sort (data) Information
  • Provides a tool with which to sort characters automatically.
• Sort Taxa (data) Information
  • Provides a tool with which to sort taxa automatically.
• Taxon Group Color Information
  • Colors by Taxon Group.
• Cell Wand (data) Information
  • Provides a tool with which to select cells in a matrix automatically.
• Select Block (data) Information
  • Provides a tool with which to select cells in a block in a matrix.
• Character Wand (data) Information
  • Provides a magic wand tool with which to select characters automatically.
• Taxon Wand (data) Information
  • Provides a tool with which to select taxa automatically.
• Align To Dropped Information
  • Supplies an alignment tool that can be used on a set of sequences. Sequences dropped by this tool on another sequence will be aligned to that other sequence (pairwise).
• Shift Dragged Sequence To Dropped Sequence Information
  • Supplies a tool that can be used on a set of sequences. Sequences dragged by this tool and dropped onto another sequence will be shifted to that other sequence (pairwise).
• Scroll To Data Information
  • Provides a tool that will scroll the data matrix to the next cell that contains data (i.e., that contains something other than a gap/inapplicable)
• Show List with Genetic Codes Information
  • Shows the List of Character window with the genetic codes column on.
• Find Sequence Information
  • Finds the next occurrence of a sequence in a matrix of molecular data.

BlockMover

• Side Pusher Information
  • Pushes all sequences on one side.
• Move block Information
  • Allows one to manually blocks in a sequence, and split the blocks.

SelectedBlockMover

• Selected Block Mover Information
  • Moves selected blocks of multiple sequences.

MultiBlockSplitter

• Splits multi-sequence block Information
  • Splits blocks of multiple sequences.

MolecDataEditorInit

• Align Sequences Information
  • Sends the selected sequence to be aligned.

DataWindowAssistantID

• Annotation Panel module Information
  • Provides tools with which to attach notes (including images) to cells of the matrix and show them.
• Character Group Color Information
  • Colors by Character Group.
• Character Reference Strip Information
  • Shows the strip at bottom of matrix with character reference.
• Color By Character Value Information
  • Colors the cells of a character matrix according to a value for the character or a moving window of characters.
• Color If Excluded Information
  • Colors the excluded characters gray.
• Color By Footnote Information
  • Colors the cells of a character matrix by whether or not they have a footnote.
• Color By Match to First Taxon Information
  • Colors the cells of a character matrix blue if they match the first taxon, yellow if different, grey if cell or first taxon has missing or inapplicable data.
• Color By State Information
  • Colors the cells of a character matrix by their contained character states.
• Color By Taxon Value Information
  • Colors the cells of a character matrix according to a value for the Taxon or a moving window of taxa.
• Assigned Colors Information
  • Provides a tool with which to color cells of a matrix.
• Information Attached To Matrix Information
  • Colors taxon names by whether or not there is information attached to this matrix.
• No Color Information
  • Turns off cell coloring.
• Selection Summary Strip Information
  • Shows the strip at bottom of matrix with character reference.
• Color For Aligning Information
  • Colors the cells of a character matrix for easy of alignment.
• Highlight Gaps in Coding Regions Information
  • Highlights gaps if site has a codon position, or if both sites to either side have codon positions, and if sites to both sides have states or missing.
• Highlight Apparently Slightly Misaligned Information
  • Colors aligned sequences to emphasize sections that seem slightly misaligned.
• Color By Amino Acid Information
  • Colors the cells of a DNA matrix by the amino acids for which they code.
• Color By Cell Value Information
  • Colors the cells of a character matrix according to a value for that cell or a moving window of cells.
• Color AAs to Check Information
  • Colors the cells of a DNA matrix by stop codons, partial triplets, and missing data.

CategDataEditorInitD

• State Names Strip Information
  • Shows the strip at bottom of matrix with state names.

DrawChart

• Bar & Line Chart Information
  • Helps make bar & line charts.
• Scattergram Information
  • Helps make scattergram charts.

CharsStatesForNodes

• Ancestral States All Information
  • Reconstructs ancestral states at nodes for all characters supplied by character source.

TraceCharacterInit

• Export Ancestral States Trace Information
  • Exports the ancestral state trace from Trace Character History.

DisplayStatesAtNodes

• Label states Information
  • A module that displays character states on tree using labels. This is a display-only module, and would be hired by another module that organizes assigning states to the nodes.
• Shade states Information
  • Shows the states at nodes by shading branches or nodes using colors, black and white, or shades of gray.

CharHistorySource

• Reconstruct Ancestral States Information
  • Reconstructs ancestral states on the nodes of a tree.
• Simulate Ancestral States Information
  • Simulates ancestral states on the nodes of a tree.

ChgSummarizerMultTrees

• State Change Summarizer (over trees) Information
  • Summarizes reconstructions of state changes of a character over a series of trees.

NumbersForNodesAndHistory

• Unambiguous Changes Information
  • Counts number of unambiguous changes along branch below based upon the character reconstruction.

aAncStatesIntro

• Ancestral States Reconstruction Package Introduction Information
  • The ancestral states reconstruction package provides modules to coordinate and display reconstruction of ancestral states on the branches of trees.

TaxonNameAlterer

• Add text to taxon names Information
  • Adds text to taxon names.
• Assign taxon names Information
  • Assigns to each taxon name a string followed by a number. For example, if the string is "g", then taxon 3 will be assigned the name g3.
• Condense taxon names Information
  • Condenses taxon names, for example for use by programs that cannot handle long names or names with punctuation.
• Prefix with Taxon Group Name Information
  • Prefixes the taxon name with the taxon group name.
• Remove from Taxon Names Information
  • Removes a specified number of characters from taxon names.
• Remove Tokens Information
  • Removes tokens from start or end of the taxon name.
• Replaces text in taxon names Information
  • Replaces text in taxon names.
• Append numbers Information
  • Appends to each taxon name the number of the taxon. This will ensure that each taxon name is unique.
• Truncate taxon names Information
  • Truncates taxon names.
• Tokenize Names Information
  • Tokenizes names. This can be useful for reading trees produced from exported files.
• Detokenize Names Information
  • Detokenizes names. This can be useful for reading trees produced from exported files.
• Move Prefix/Suffix of Taxon Name Information
  • Moves the suffix of the taxon name to be to prefix or the prefix to be the suffix
• Keep Only Prefix/Suffix of Taxon Name Information
  • Keeps only Prefix or Suffix of Taxon Name.
• Remove Prefix/Suffix of Taxon Name Information
  • Remove Prefix or Suffix of Taxon Name.
• Rename Taxa Based On Table in File Information
  • Renames the taxa based upon chosen columns in a tab-delimited text file, using OTU IDs or curent taxon names to find the relevant row within that file.
• Simplify Taxon Names Information
  • Simplifies taxon names so that they will work with MrBayes, RAxML, etc..
• Alphabetic taxon names Information
  • Assigns as the taxon names the roman alphabet in sequence, with Z followed by A1 etc..

DefaultsAssistant

• Set Author Information
  • Sets the author for this machine and account.
• Unique IDs default Information
  • Sets the preferences for storing unique ids.
• NEXUS Defaults Information
  • Sets whether TITLE and LINK commands are to be suppressed where possible in saving NEXUS files.
• Set Tree Defaults Information
  • Sets the default state for polytomies & other aspects of tree handling.

ParametersExplorer

• Parameters Explorer Information
  • Provides a window to show values returned when parameter settings are varied

StringMatcher

• Default String Matcher Information
  • Uses the default string-matching mechanism of the module that is doing the calling.

TaxaPartitionSource

• Current taxa partition Information
  • Supplies the current taxa partition.
• Taxa partition from Taxa associations Information
  • Constructs a taxa partition from an association.

TaxonUtility

• Delete Footnotes from Taxa Information
  • Deletes footnotes from taxa
• Duplicate Taxa Information
  • Duplicates selected taxa and their character states.
• Merge Selected Taxa Information
  • Merges selected taxa and their character states.
• Randomize Taxon Order Information
  • Randomizes the order of taxa.

TaxonSelector

• Select Taxa from List In File Information
  • Select all taxa whose names appear in a list in a simple text file. The file should consist of one column, listing the names.
• Select Taxa from Name Search Information
  • Select taxa based upon a name search.

EditRawNexusBlock

• Raw Nexus block editor Information
  • Edits blocks in a NEXUS file.

TextDisplayer

• Show text Information
  • Shows text in a window

TaxonPairSource

• Stored Taxon Pairs Information
  • Supplies taxon pairs stored, for instance in a file.

TaxaSelectCoordinator

• Taxon selection coordinator Information
  • Coordinates taxon selection.

OTUIDCodeInfoCoord

• Coordinator of voucher information Information
  • Finds suppliers of voucher information.

OTUIDCodeInfoSource

• Voucher Info from Flexible Table Information
  • Supplies voucher information from a flexible tab-delimited table in a text file.

aBasicIntro

• Basic Utilities Package Introduction Information
  • Provides basic utilities for Mesquite.

DataAlterer

• Remove Invariant Characters Information
  • Removes all characters that have one state or fewer.
• Fill Information
  • Fills cells with a uniform state in a character data editor.
• Impose Indel Pattern of Other Matrix Information
  • Converts each cell in a matrix to a gap (inapplicable) if the equivalent cell in another matrix has a gap.
• Shuffle states among taxa Information
  • Alters data by shuffling states among taxa within a character.
• Reverse Sequence Information
  • Alters data by reversing sequence of states.

MeristicDataAlterer

• Random Fill (Meristic Uniform) Information
  • Fills cells with a random state, uniformly.

DNADataAlterer

• Shift to Minimize Stop Codons Information
  • Shifts each sequence by 0, 1, or 2 bases to minimize number of stop codons implied.
• Convert to RY Information
  • Converts nucleotide data to RY data in selected region.
• Nucleotide Complement Information
  • Alters nucleotide data to its complement.
• Set to Lower Case Information
  • Alters nucleotide data to lower case coding (e.g, to indicate less certain).
• Set to Upper Case Information
  • Alters nucleotide data to upper case coding (e.g, to indicate more certain).
• Remove Terminal Incomplete Codons Information
  • Removes any incomplete codons from the start and end of each sequence.

MolecularDataAlterer

• Remove Gaps-Only Characters Information
  • Removes all characters that are gaps only.
• Collapse Sequences to Left (Remove all Gaps) Information
  • Collapses sequences in the selected block of cells to yield unaligned sequences, by removing all gaps.
• Collapse Sequences to Right (Remove all Gaps) Information
  • Collapses gaps in the selected block of cells to the right, to yield unaligned sequences.
• Remove Terminal Gaps-Only Characters Information
  • Removes characters at edges of matrix that are gaps only.

DNADataAltererCon

• Align DNA to Protein Information
  • Realigns a DNA matrix to match the alignment in an amino acid alignment.
• Reverse Complement Information
  • Reverses the DNA sequence and complements the bases.

ContDataAlterer

• Add Character Information
  • Alters continuous data by adding a continuous character from a source of characters. All items of the matrix are similarly modified.
• Add Noise (Gaussian) Information
  • Adds normally distributed noise to existing states. Only the first item of a continuous matrix is modified.
• Add value Information
  • Alters continuous data by adding a value. All items of the matrix are similarly modified.
• Arcsine transform Information
  • Alters continuous data by arcsine transforming values.
• Inverse of Value Information
  • Alters continuous data by inverting values (new value = 1/(original value)).
• Log transform Information
  • Alters continuous data by log transforming values.
• Multiply by character Information
  • Alters continuous data by multiplying by a continuous character. All items of the matrix are similarly modified.
• Multiply by value Information
  • Alters continuous data by multiplying by a value. All items of the matrix are similarly modified.
• Random Fill (Gaussian/Normal) Information
  • Fills cells with a random state, using a Normal distribution.
• Random Fill (Uniform) Information
  • Fills cells with a random state, uniformly.
• Square Root transform Information
  • Alters continuous data by taking the square root.
• Standardize Information
  • Alters continuous data by standardizing to have mean = 0 and unbiased estimate of variance = 1. Modifies only the first item of a multi-item matrix

CategDataAlterer

• Convert Uncertainties to Polymorphisms Information
  • Alters categorical data by converting uncertain entries to polymorphisms.
• Convert Uncert./Polymorph. to Missing Information
  • Alters categorical data by converting uncertain or polymorphic entries to missing data.
• Convert Polymorphisms to Uncertainties Information
  • Alters categorical data by converting polymorphic entries to uncertainties.
• Arbitrarily Resolve State Ambiguities Information
  • Alters categorical data by arbitrarily resolving ambiguous sites to one of the possible states.
• Add Characters from Source Information
  • Adds characters from a source of characters.
• Random Fill (Categorical) Information
  • Fills cells with a randomly-chosen state. For DNA data, states A, C, G, and T are chosen with equal probability; for other data, states up to and including the maximum state value are chosen with equal probability.
• Sprinkle Missing in Cells Information
  • Fills cells with a missing data with a specified probability.
• Recode Characters Information
  • Recodes categorical data (e.g., state 1 to state 0).
• Shift Other To Match Selected Information
  • Shifts other sequences to match the one selected.
• Clean Up Matrix Information
  • This will adjust sequences according to the option chosen (e.g., by reverse complementing, aligning the matrix, and then adjusting the codon postions).
• Gaps<->Missing Information
  • Converts gaps to missing data or vice versa.
• Align Sequences in Matrix Information
  • Performs mulitple sequence alignment using an available aligner.

BooleanForCharacter

• Variable (Mult. States) Information
  • Indicates whether a character has multiple observed states. If taxa are selected, only the selected taxa are examined.
• Character Included Information
  • A boolean that is true if a character is currently included, and false if the character is currently excluded.
• Parsimony Informative Information

DataColumnNamesAssistant

• Consensus Sequence Strip Information
  • Displays a consensus sequence as in info strip in a character matrix editor.
• Boolean Info Strip Information
  • Shows an strip of boxes near the top of each a character column that shows the value of a boolean for that character in gray or white.
• Number of Data Cells Strip Information
  • Displays the number of cells in a character containing data as an info strip in a character matrix editor.

CategStateForCharacter

• Consensus State for Character Information

CharMatrixManager

• Manage categorical character matrices Information
  • Manages categorical data matrices (including read/write in NEXUS file).
• Manage Continuous char. matrices Information
  • Manages continuous data matrices (including read/write in NEXUS file).
• Manage Geographic character matrices Information
  • Manages data matrices of geographic data (including read/write in NEXUS file).
• Manage Meristic char. matrices Information
  • Manages meristic data matrices (including read/write in NEXUS file).

CategMatrixManager

• Manage DNA/RNA matrices Information
  • Manages DNA/RNA data matrices (including read/write in NEXUS file).
• Manage Protein matrices Information
  • Manages Protein data matrices (including read/write in NEXUS file).

NumberForTaxon

• Proportion Unique States in Taxon Information
  • Reports the proportion of unique states in a taxon for a data matrix.
• Number of Matrices with Data for Taxon Information
  • Reports for how many matrices the taxon has data.
• Alignment Score To Ref. Information
  • Reports the Alignment Score for a taxon in a data matrix. The score for each taxon is the cost of aligning that taxon's sequence against the reference taxon using Mesquite's default pairwise aligner. Lower scores mean a better alignment.
• Align Score/RC Align Score To Ref. Information
  • Reports the Alignment Score / Reverse Complement Alignment Score for a taxon in a data matrix. The score for each taxon is the cost of aligning that taxon's sequence against the reference taxon using Mesquite's default pairwise aligner, divided by the score for aligning the reverse complement of the sequence against the reference. Scores greater than one mean that alignment is better if one of the sequences is reverse complemented .
• Multistate sites in taxon Information
  • Reports the number of polymorphic/partially uncertain sites in a taxon for a data matrix.
• Number of Stops Information
  • Reports the number of stops coded by nucleotides in a taxon for a data matrix.
• Proportion Gaps in Taxon Information
  • Reports the proportion of gaps (inapplicable codings) in a taxon for a data matrix.
• Proportion lower case codings in taxon Information
  • Reports the percentage of lower case codings in a taxon for a data matrix.
• Proportion missing data in taxon Information
  • Reports the proportion of missing data in a taxon for a data matrix.
• Proportion of ambiguous sites in taxon Information
  • Reports the proportion of polymorphic/partially/fully uncertain sites in a taxon for a data matrix.
• Number of Unambiguous Sites in Sequence Information
  • Reports the number of unambiguous sites.
• Sequence Length Information
  • Reports the length (total minus gaps) of a molecular sequence in a taxon.
• Average Taxon Value among Trees Information
  • Averages among trees a value calculated for a taxon using a tree.
• Value from Tree Information
  • Calculates a value for each taxon using a tree.
• Taxon Instability Among Trees Information
  • Calculates for each taxon the degree to which its implied unweighted patristic distances between that taxon and others differs among trees. For each taxon i this sums over all tree pairs x and y and over all other taxa j: | Dijx - Dijy |/(Dijx + Dijy)^^z where Dijq is the distance between taxa i and j on tree q. Close relationships are emphasized if the exponent z is higher (default is 2).

NumberForTaxonIncr

• Continuous state of taxon Information
  • State of a continuous character.

MatrixInfoPanelAssistantI

• Small State Names Editor Information
  • Edits character state names within the editor info panel.
• Continuous Items Editor Information
  • Edits items for continuous data matrix within the editor info panel.
• Meristic Items Editor Information
  • Edits items for meristic data matrix within the editor info panel.
• Sequence Information Editor Information
  • Edits character state names within the editor info panel.

aCategIntro

• Categorical Data Package Introduction Information
  • Provides basic facilities for handling categorical characters.

FileProcessor

• Alter All Matrices Information
  • Manages data-transforming modules to transform all matrices in a file.
• Compile Processed Matrices into One File Information
  • Compiles matrices from each file processed into a combined NEXUS file.
• Process using Data Utility Information
  • Manages data-transforming Data Utility modules to transform all matrices in a file.
• Calculate Number for Matrices Information
  • Manages number calculating modules for all matrices in a file.
• Export Matrices Information
  • Manages file exporting modules to export all matrices in a file.
• Alter Taxon Names Information
  • Manages taxon renaming for file processing.
• Compile Trees in Nexus Block in file Information
  • Compiles trees from this file into a text file with a nexus tree block.
• Compile Trees into Simple File Information
  • Compiles trees from this file into a simple text file.
• Make Trees and Add to File Information
  • Manages tree block filling as an alteration to a file.

DatasetsListUtility

• Alter Matrix As Utility Information
  • Alters selected matrices in List of Character Matrices window.
• Concatenate Selected Matrices Information
  • Concatenates selected matrices in List of Character Matrices window. Only those compatible with first selected are concatenated into it.
• Duplicate Selected Matrices Information
  • Duplicates selected matrices in List of Character Matrices window.

CharMatrixFiller

• Matrix from Clipboard Information
  • Makes a character matrix from text in the clipboard.

CharMatrixSource

• Alter Matrix Information
  • Supplies character matrices that are altered from an existing matrix.
• Concatenate Respective Matrices from Two Sources Information
  • Supplies matrices by concatenating respective matrices from two sources. The i'th matrix supplied is the concatenation of the i'th matrix from each of the two sources. Assumptions like weights and character models are NOT transferred. For categorical data, state names are not included. For continuous data, new items may need to be created to accommodate differences in items between the matrices.
• Condense to Matrix of Patterns Information
  • Condenses a categorical matrix to one having exactly one character of each pattern with that character weighted by the number of copies of that pattern in the original matrix.
• Randomly Modify Respective Matrices Information
  • Supplies character matrices that are randomly modified from a series of existing matrices. The i'th modified matrix is derived from the i'th original matrix.
• Randomly Modify Matrix Information
  • Supplies character matrices that are randomly modified from an existing matrix.
• Stored Matrices Information
  • Supplies character matrices from data files (as opposed to simulated characters, for example).
• Compact to (X,Y) matrix Information
  • Converts a matrix of alternating X and Y columns (e.g. for landmarks) to a matrix each cell of which has X,Y values.
• Simulated Matrices on Trees Information
  • Supplies simulated character matrices, each evolved on a different of a series of trees.
• Simulated Matrices on Current Tree Information
  • Supplies simulated character matrices.
• Translate DNA to Protein Information
  • Translates a stored DNA matrix to protein.
• Matrices from Ordinations Information
  • Supplies character matrices from ordinations of existing matrices.
• MRP Matrices from Trees Information
  • Supplies matrices which represent trees for MRP (Matrix Representation with Parsimony) supertree analyses.

RandomMatrixModifier

• Bootstrap Resample Matrix Information
  • Resamples characters from a matrix for use in bootstrap methods.
• Rarefy Characters Information
  • Deletes characters randomly to rarefy matrix.
• Reshuffle States Within Characters Information
  • Shuffles (permutes) character states among taxa within each character.
• Reshuffle Within Characters (Taxa Partitioned) Information
  • Shuffles (permutes) character states among taxa of each taxa partition, within each character.
• Reshuffle Within Taxa (Char. Partitioned) Information
  • Shuffles (permutes) character states among characters of each character partition, within each taxon.
• Reshuffle States Within Taxa Information
  • Shuffles (permutes) character states among characters within each taxon.
• Sprinkle Missing Information
  • Randomly converts entries in the character matrix to missing data, with a certain probability (i.e., it "sprinkles" missing data around the matrix).

MatrixSourceCoord

• Matrix Source (indep.) Information
  • Coordinates the supply of matrices to other modules. It acts independently, in that it decides what matrix to supply (e.g., by presenting an interface to choose).

MatrixSourceCoordObed

• Matrix Source (obed.) Information
  • Coordinates the supply of matrices to other modules. It acts obediently, in that it does not present an interface to choose which matrix, but relies on employer to decide.

CharSelectCoordinator

• Character selection coordinator Information
  • Coordinates character selection.

CharSourceCoord

• Character Source Information
  • Coordinates the supply of characters from various sources of characters.

CharSourceCoordObed

• Character Source Information
  • Coordinates the supply of characters from various sources of characters.

DataUtility

• Compare Other Matrix Information
  • Compares matrix in data editor with another.
• Concatenate Other Matrix Information
  • Concatenates matrix onto one in data editor. Assumptions like weights and character models are NOT transferred. For categorical data, state names are not included. For continuous data, new items may need to be created to accommodate differences in items between the matrices.
• Log Matrix Details Information
  • Writes to log details about the matrix, including its states checksum.
• Fetch & Add GenBank Sequences Information
  • Fetches GenBank nucleotide sequences given their GenBank accession numbers and adds them to the matrix.

DNADataUtility

• Compare Bases with Taxon Information
  • Compares nucleotide bases of selected taxa with those of a chosen taxon.

ContDataUtility

• Add item... Information
  • Adds an item in each cell of a continuous matrix.
• Discretize Selected Characters... Information
  • Bins the selected continuous characters to discretize them into categorical characters (ordered if more than two states), and adds them to an existing categorical matrix. If the continuous matrix is multi-item, only the first item is used.
• Remove item... Information
  • Removes an item in each cell of a continuous matrix.
• Rename item... Information
  • Renames an item of a continuous matrix.

ManageDATAblock

• Read DATA blocks Information
  • Coordinates the reading of a DATA block in NEXUS file.

CharacterSelector

• Character Ranges... Information
  • Selects characters that are within the ranges given in a text list of the form [start end] [start end]...
• With probability p Information
  • Selects characters randomly with probability p.
• With State Distinguishing Selected Taxa Information
  • Selects characters that have a character state that is unique to and uniform in the selected taxa, as possible synapomorphic or diagnostic states for the set of taxa.
• Random n characters Information
  • Selects n characters randomly.
• Variable among taxa Information
  • Selects characters that are variable among the selected taxa
• Interpolate Character Selection Information
  • Selects characters that are surrounded by characters selected.
• GBLOCKS Selector Information
  • Selects characters according to an extended version of the GBLOCKS algorithm (Castresana, 2000).

CharListAssistant

• Stored Character Order Information
  • Supplies current order applied to characters for character list window.
• Boolean for Character (in List of Characters window) Information
  • Supplies booleans for characters for a character list window.
• Current Codon Positions Information
  • Supplies current codon positions applied to characters for character list window.
• Character Inclusion Information
  • Shows current character inclusion in character list window.
• Group Membership (characters) Information
  • Lists and allows changes to group membership in the current partition of characters, for List of Characters window.
• Unique ID (characters) Information
  • Shows unique id assigned to character.
• Current Weights Information
  • Supplies current weights applied to characters for character list window.
• Number for Character (in List of Characters window) Information
  • Supplies numbers for characters for a character list window.
• Character Set Membership Information
  • Shows, in the character list window, the character sets to which a character belongs.
• States Information (in List of Characters window) Information
  • Supplies basic character state information for characters in character list window.
• Default Order (characters) Information
  • Shows default order of character.
• Current Parsimony Models Information
  • Shows current parsimony models applied to characters in character list window.
• Current Probability Models Information
  • Supplies current stochastic models applied to characters for character list window.
• Current Genetic Codes Information
  • Shows current genetic codes applied to characters in character list window.

aCharMatricesIntro

• Character Matrices Package Introduction Information
  • Provides basic management and utilities for character data matrices.

ItemsCharter

• Item values chart Information
  • Manages chart of values for items.

ItemsBiplotter

• Items bi-plot Information
  • Makes a chart comparing two values for each of many items.

HistogramAssistantA

• Display Mean Information
  • Calculates and shows the mean value.
• Show Percentile Information
  • Calculates and shows percentile boundaries. Finds the upper (right) or lower (left) tail of the distribution that contains the specified percentage of the distribution. If there is not a boundary that exactly matches the specified percentage, then the closest boundary that does not exceed the percentage is shown.

ScattergramAssistantA

• Show Y = X Information
  • Shows the Y=X line on a scattergram

aChartsIntro

• Charting Package Introduction Information
  • Provides basic charting functions.

aContIntro

• Continuous Data Package Introduction Information
  • Provides basic facilities for handling continuous-valued characters.

CharSubmodelCurator

• Codon Position Rates Model Information
  • Defines and maintains models that specify rates for codon positions.
• Gamma Rates Model Information
  • Defines and maintains Gamma rate variation models.
• Gamma Invar Rates Model Information
  • Defines and maintains Gamma rate variation models with a proportion of invariable characters.
• Proportion Invariable Model Information
  • Defines and maintains models that specify that a certain proportion of characters are invariable.
• GTR Rate Matrix Model Information
  • Defines and maintains six-parameter general time-reversible (GTR) rate matrix models.
• Ti/Tv Rate Matrix Model Information
  • Defines and maintains two-parameter rate matrix models with a transition and transversion rates.
• DNA Empirical State Frequencies Model Information
  • Defines and maintains model of state frequencies that match those found in an empirical matrix.
• User-Specified Nucleotide Frequency Model Information
  • Defines and maintains user-specified nucleotide frequency models.

CharacterSimulator

• Evolve DNA Characters Information
  • Simulates evolution of DNA sequences on a tree.
• Evolve Categorical Characters Information
  • Simulates character evolution for categorical characters on a tree.
• Evolve Continuous Characters Information
  • Simulates character evolution for continuous characters on a tree.

WholeCharModelCurator

• Stepmatrix Information
  • Supplies editor for and manages stepmatrices (cost matrices).
• Brownian Model Information
  • Initializes Brownian motion character model for likelihood and other probability calculations.

CategProbModelCurator

• Composite DNA Simulation Model Information
  • Defines and maintains simple stochastic models of DNA evolution for simulations.
• Asymmetrical 2-param. Markov-k Model Information
  • Defines and maintains simple Markov k-state asymmetrical 2-parameter stochastic models of character evolution.
• Mk1 Model (Markov 1 parameter) Information
  • Defines and maintains simple Markov k-state 1-parameter stochastic models (Lewis, 2001) of character evolution.

aGenesisIntro

• Genesis Introduction Information
  • Implements stochastic models of molecular evolution.

aIOIntro

• Import and Export Package Introduction Information
  • Provides file import/export utilities.

TaxonListAssistant

• Boolean for Taxon (in List of Taxa window) Information
  • Supplies booleans for taxa for a taxon list window.
• Default Order (taxa) Information
  • Shows default order of taxa.
• Mark Taxa Information
  • Permits user to mark taxa in the List of Taxa with a specific name.
• Number for Taxon (in List of Taxa window) Information
  • Supplies numbers for taxa for a taxa list window.
• Unique ID (taxa) Information
  • Shows unique id assigned to taxon.
• Alternative Names Information
  • Lists the alternative names for the taxon.
• Group Membership (taxa) Information
  • Lists and allows changes to group membership in the current partition of taxa, for List of Taxa window.
• OTU ID Code Information
  • Lists the OTU ID code for a taxon.
• OTU ID Code Database Information
  • Lists the OTU code database for a taxon.
• Associated Taxa Information
  • Lists and edits what other taxa (e.g. contained or containing) are associated with these.
• Original File (import source) Information
  • Shows the orignal file from which a fuse/imported taxon came.
• GenBank Number Information
  • Lists the GenBank accession number of a sequence in a matrix.
• Publication Code Information
  • Lists the publication code for a sequence.
• Has Data in Matrix Information
  • Indicates whether taxon has non-missing non-gap data in a given matrix.

TreeListAssistant

• Boolean for Tree (in List of Trees window) Information
  • Supplies booleans for trees for a trees list window.
• Number for Tree (in List of Trees window) Information
  • Supplies numbers for trees for a trees list window.
• Attachment Information
  • Displays an item attached to trees.
• Polytomy Assumption Information
  • Indicates whether the tree assumes that any polytomies, if present, are hard or soft. If not, the default assumption is used.
• Polytomies Present Information
  • Indicates whether polytomies are present.
• Rooting status Information
  • Indicates whether the tree is rooted or unrooted.

CharGroupListAssistant

• Character Group Color in List Information
  • Shows color assigned to character group.

CharInclSetListAsst

• Number of characters in inclusion set Information
  • Indicates number of characters in inclusion set in list window.

CharListAssistantI

• Annotation Panel module (list of characters) Information
  • Provides tools with which to attach notes (including images) to characters and show them.

CharSetListAsst

• Number of characters in character set Information
  • Indicates number of characters in character set in list window.

TaxaListAssistantI

• Color Taxa Information
  • Provides paintbrush to color taxon names.
• Annotation Panel module (list of taaa) Information
  • Provides tools with which to attach notes (including images) to characters and show them.
• Show Columns for All Matrices Information
  • Shows the Has Data column for all matrices.

DataSetsListAssistant

• Type of character data matrix Information
  • Indicates type of character data matrix (e.g., continuous, DNA, etc.).
• Number of characters of data matrix Information
  • Indicates taxa of data matrix.
• Taxa of data matrix Information
  • Indicates taxa of data matrix.
• Editability of Matrix Information
  • Indicates whether editing of the matrix is allowed or inhibited.
• Visibility of Matrix Information
  • Indicates whether character data matrix is hidden or not.
• Number for Matrix (in List of Character Matrices window) Information
  • Supplies numbers for character matrcies for a character matrices list window.

ModelsListAssistant

• Data type for model Information
  • Indicates data type of model in list window.
• Model Paradigm Information
  • Indicates paradigm of model in list window.
• Type of Model Information
  • Indicates type of model (e.g., Mk1, step-matrix) in list window.
• Whole or Submodel Information
  • Indicates whether model is a complete or partial model of character evolution.

TreeblocksListAssistant

• Number for Tree Block (in List of Tree Blocks window) Information
  • Supplies numbers for tree blocks for a tree blocks list window.
• Number of trees in tree block Information
  • Indicates number of trees.
• Taxa of tree block Information
  • Indicates taxa of tree block.

TaxaPartListAssistant

• Number of groups in taxa partition Information
  • Indicates number of groups in taxa partition in list window.

TaxaSetListAssistant

• Number of taxa in taxa set Information
  • Indicates number of taxa in taxa set in list window.

TaxaBlocksListAssistant

• Number of taxa in set Information
  • Indicates number of taxa in list window.

TaxonGroupListAssistant

• Taxon Group Colors Information
  • Shows color assigned to taxon group.
• Number of Taxa Assigned to Group Information
  • Shows the number of taxa assigned to each taxon group.
• Taxon Group Symbol Information
  • Shows symbol assigned to taxon group.
• Taxon Group Symbol Size Information
  • Shows size of symbol assigned to taxon group.
• Taxon Group Visibility in Taxa Maps Information
  • Shows whether or not a taxon group is shown on a taxa map.

aListsIntro

• List Windows Package Introduction Information
  • Provides List windows to manage taxa, characters and other information.

MesquiteInit

• Defaults Information
  • Supervises some Mesquite-wide defaults
• Installer Information
  • Installs packages.
• Utilities Information
  • Provides a menu for utilities

SimplicityManagerModule

• Simplicity Manager Information
  • A small module to supervise the interface for simplification management.

BrowseHierarchy

• DrawHierarchy Information
  • Draws project and module trees

ManageForeignBlocks

• Manage Foreign Blocks Information
  • Manages unrecognized blocks in a NEXUS file.

GeneralFileMaker

• Open Special NEXUS Information
  • Opens a NEXUS file with a special importer
• Open URL Information
  • Opens a file on the web as if it were a local data file
• Process Data Files Information
  • Processes a folder of data files.
• Tree from ToL Web Project... Information
  • Gets the tree for the page of the Tree of Life Web Project for the group specified.

EmployeeTree

• Show Employee Tree Information
  • Shows the window listing the tree of employees of the module of a given window.

TaxonSource

• Stored Taxa Information
  • Supplies taxa stored, for instance in a file.

WindowHolder

• Window Holder Information
  • Helps other modules by holding their windows.

CharStatesForNodes

• Parsimony Ancestral States Information
  • Coordinates the parsimony reconstruction of ancestral states.
• Likelihood Ancestral States Information
  • Coordinates reconstruction of ancestral states by maximum likelihood. Currently each node is estimated independently (i.e., corresponding to PAUP's marginal reconstruction).
• Stochastic Character Mapping (Categorical) Information
  • Coordinates reconstruction of ancestral states using stochastic character mapping.

ParsAncStatesForModel

• Parsimony Stepmatrix Information
  • Reconstructs ancestral states of categorical characters using a stepmatrix (cost matrix).
• Parsimony Linear Information
  • Reconstructs the ancestral states of continuous characters so as to minimize the sum of absolute values of changes (linear, Wagner, Farris or Manhattan parsimony). If the continuous character has multiple items, then length is reported on only the first item.
• Parsimony Ordered Information
  • Reconstructs the ancestral states of categorical characters using parsimony, under the assumption that states are ordered (ordered, Farris or Wagner parsimony; additive). Also counts parsimony steps.
• Parsimony Squared-change Information
  • Reconstructs the ancestral states of continuous characters so as to minimize the sum of squared changes (squared-change or least squares parsimony; Brownian motion likelihood).
• Parsimony Unordered Information
  • Reconstructs the ancestral states of categorical characters using parsimony, under the assumption that states are unordered (unordered or Fitch parsimony; nonadditive). Also counts parsimony steps.
• Parsimony Meristic Linear Information
  • Reconstructs the ancestral states of mersitic characters so as to minimize the sum of absolute values of changes (linear, Wagner, Farris or Manhattan parsimony). If the meristic character has multiple items, then length is reported on only the first item.

aParsimonyIntro

• Parsimony Package Introduction Information
  • Preforms parsimony calculations to count steps and treelength of characters on trees.

aStochCharIntro

• Stochastic Character Evolution Package Introduction Information
  • Provides stochastic models and simulations of character evolution.

MargLikeAncStCLForModel

• Maximum likelihood reconstruct (Generic categorical) Information
  • Assesses likelihood for categorical characters, and r econstructs ancestral states by the maximum marginal probability ("MLE") criterion

TreeAlterer

• Add Taxa To Tree Information
  • To a tree with some taxa excluded, adds taxa.
• Search for Better Tree Information
  • Finds better trees (by the chosen optimality criterion) by rearranging the current tree.

TreeAltererMult

• Collapse Zero-length Branches Information
  • Collapses zero-length branches to yield polytomes.
• Resolve Polytomies (to 0-length branches) Information
  • Resolves polytomies arbitrarily and assigned the resulting new branches zero length.
• Set Polytomy Assumption to Default Information
  • Sets assumption that any polytomies in the tree are whatever is current default (which can be set in the submenu File>Defaults>Tree Defaults).
• Set Polytomy Assumption to Hard Information
  • Sets assumption that any polytomies in the tree are hard.
• Set Polytomy Assumption to Soft Information
  • Sets assumption that any polytomies in the tree are soft.
• Set to Arbitrary Symmetrical Information
  • Sets the tree to an arbitrary symmetrical tree.
• Right-Ladderize Tree Information
  • Sets the tree to its ladderized (right) version.
• Root tree Information
  • Sets the tree to rooted.
• Unroot tree Information
  • Sets the tree to unrooted.
• Add Selected Taxa To Tree Information
  • To a tree with some taxa excluded, adds those taxa that are selected.
• Cut Selected Taxa from Tree Information
  • Cuts the selected taxa from the tree.
• Delete Reticulations Information
  • Deletes secondary parents of nodes with more than one immediate ancestor. There is no control over which parents get deleted.
• Graft Other Tree Information
  • Grafts a tree in a tree window onto given tree; requires that the other tree includes none of the same terminal taxa. If a taxon in receiving tree is selected, graft occurs there; otherwise, graft occurs at root.
• Root tree with selected taxa as outgroup Information
  • Roots the tree between the selected taxa and the remainder, if possible.
• Reinterpret Internal Node Labels... Information
  • Reinterprets labels from all internal nodes as numbers or text attached to nodes or branches.
• Remove Internal Node Labels Information
  • Deletes labels from all internal nodes.

BranchLengthsAlterer

• Scale Selected Branch Lengths Information
  • Adjusts lengths of a tree's selected branches by multiplying them by an amount.
• Assign Selected Branch Lengths Information
  • Assigns a value for branch length for all of a tree's selected branches.
• Obtain Branch Lengths from Values Attached to Nodes Information
  • Assigns branch lengths to the tree taken from values already attached to nodes, for instance support values or divergence times from other programs.

BranchLengthsAltererMult

• All Branch Lengths to 1.0 Information
  • Assigns a value of 1.0 for branch length for all of a tree's branches.
• All Unassigned Branch Lengths to 1.0 Information
  • Assigns a value of 1.0 for branch length for all of a tree's branches that have not yet had a branch length assigned.
• Enforce Minimum Node Age Constraints Information
  • Uses minimum node age constraints to set the branch lengths on the tree.
• Deassign Branch Lengths Information
  • Sets lengths of a tree's branches to unassigned.
• Convert Negative Branch Lengths to Zero Information
  • Adjusts a tree's branch lengths so that negative branch lengths are zero
• Obtain Branch Lengths from Numbers For Nodes Information
  • Assigns a value of branch length for all of a tree's branches based upon the numbers calculated by a Numbers for Nodes.
• Scale All Branch Lengths Information
  • Adjusts a tree's branch lengths by multiplying them by an amount.
• Assign All Branch Lengths Information
  • Assigns a value for branch length for all of a tree's branches.
• Assign Branch Lengths From Node Names Information
  • Assigns a value for branch length for all of a tree's branches based upon node names that represent numbers.
• Assign Branch Lengths Less than or Equal to Zero... Information
  • Assigns a user-provided value to all branches with lengths less than or equal to zero.
• Arbitrarily Ultrametricize Information
  • Adjusts a tree's branch lengths so that the distances among terminal taxa are ultrametric (i.e. like a molecular clock, all tips reaching to same level). This is not done with any sophisticated smoothing algorithm; rather, branches are just stretched until they reach to same level.
• Branch Lengths from current, reinterpreted as Divergence Times Information
  • Reassigns branch lengths under the assumption that currently assigned branch lengths are actually divergence times.

TreeListUtility

• Alter Branch Lengths Information
  • Alters branch lengths of selected trees.
• Alter Trees Information
  • Alters selected trees.
• Extract tree block Information
  • Extracts selected trees and places them in a new tree block.

NumberForTreeBlock

• Average Tree Value Information
  • Calculates the average of some value for trees in a tree block.
• Number of Trees Matching Criterion Information
  • Counts the number of trees in a tree block that match a user-specified criterion. For example, it could count the number of trees in a tree block which are congruent with a particular tree topology (by selecting the "Tree Congruent with Specified Tree Topology" module in the Criterion for Trees dialog).

NForTaxonWithTree

• Branch Length from Root Information
  • For each taxon, calculates the sum of the branch lengths from that taxon to the root of the tree.
• Terminal Branch Length Information
  • For each taxon, calculates the length of the terminal branch on the tree, if present. If a taxon is a descendant of a dichotomous root in a tree with more than 2 taxa, then the length of the other descendant is also added in. .

BranchNamesAltererMult

• Clear All Node Names Information
  • Clears all node names from the tree.

TaxonNameStyler

• Color by Assigned Color Information
  • Supplies the colors assigned individually to the taxa.
• Color by Taxon Group Information
  • Supplies the colors assigned to the taxon's group (partition).
• No Color for Taxon Information
  • Supplies no color for the taxon.
• Emphasize Taxa With Data in More Matrices Information
  • Supplies the colors and boldness proportional to the number of matrices for which the taxon has data.
• Color Taxa By Number Information
  • Supplies the color for a taxon name according to a number calculated for the taxa.

TreeSourceDefinite

• Definite Tree Source Information
  • Supplies trees from from a tree source, arranged to be a definite number

TreeSimulate

• Uniform speciation (Yule) Information
  • Generates tree by simple uniform probability speciation (a Yule process) as done by Harding (1971). The chance of speciation is equal for all tips.
• Equiprobable Trees Information
  • Generates trees randomly so that each possible labelled tree topology is equally likely.
• Coalescence in Current Tree with Migration Information
  • Generates tree by a simple coalescence model of a neutral gene with constant population size, within a current species tree from a Tree window or other tree context. Branch lengths are assigned according to generation of coalescence. The default population size is 10000. The species tree used is a current tree found in a Tree Window or other tree context. Migration is allowed; the default probability is 0.00001 per individual generation. Migration can be isolated to a particular generation, or spread throughout the depth of the species/population history.
• Coalescent Trees Information
  • Generates tree by coalescence within a single panmictic population.
• Coalescence Contained within Current Tree Information
  • Generates tree by a simple coalescence model of a neutral gene with constant population size, within a current species tree from a Tree window or other tree context. Branch lengths are assigned according to generation of coalescence.The species tree used is a current tree found in a Tree Window or other tree context.
• Birth/Death Process Trees Information
  • Generates tree by simple birth/death model with a constant rate of speciation (birth) and of extinction (death).
• Uniform Speciation with Sampling Information
  • Generates tree by simple uniform probability speciation (a Yule process), with subsequent sampling of species.

TreeBlockSource

• Tree Blocks from Files Listed In File Information
  • Supplies tree blocks in files listed in a file.
• Other Tree Blocks Information
  • Supplies blocks of trees from various sources
• Simulated Tree Blocks Information
  • Creates a tree block of simulated trees.
• Stored Tree Blocks Information
  • Supplies lists of trees stored, for instance in a file.
• Tree Block Directly From File Information
  • Supplies a block of trees directly from a file

NumberFor2Characters

• Value for 2 characters with current tree Information
  • Coordinates the calculation of a number for two characters based on a current tree.

NumbersForNodesAndMatrix

• Numbers for Nodes from Character Reconstructions Information
  • Supplies numbers, based on a character reconstruction, for each node of a tree.

TWindowMaker

• Simple Tree Window Information
  • Displays a single tree.
• Dependent Contained Tree Window Information
  • Displays a single tree (the same as contained within a tree in a tree window).

DisplayNumbersAtNodes

• Shade numbers Information
  • A module that displays numbers at tree nodes using labels. This is a display-only module, and would be hired by another module that organizes assigning numbers to the nodes.

TreeListInit

• Show Tree Information
  • Provides tool in the List of Trees window to request that tree be shown in window.

TreeInfoPanelAssistant

• Values (Tree information panel)... Information
  • Makes the Values section of the Tree Information Panel to display values pertaining to the tree.

OneTreeSource

• Tree of context Information
  • Supplies a single tree from the nearest tree context (e.g., an available tree window).

aTreesIntro

• Trees Package Introduction Information
  • Basic management and utilities for phylogenetic trees.

MultipleSequenceAligner

• ClustalW Align Information
  • Sends the selected sequence to ClustalW to align.
• MAFFT Align Information
  • Sends the selected sequences to MAFFT to align.
• MUSCLE Align Information
  • Sends the selected sequence to Muscle to align.

aAlignIntro

• Align Package Manual Information
  • Align is a Mesquite package providing tools for the alignment of sequence data.

ManageDistributionBlock

• Read DISTRIBUTION blocks Information
  • Coordinates the reading of a DISTRIBUTION block in NEXUS file.

AssociationSource

• Stored Taxa Associations Information
  • Supplies associations between taxa that are stored, for instance in a file.

aAssocIntro

• Taxa Association Package Introduction Information
  • Provides utilities for managing taxa associations (e.g. for gene/species analyses).

ChartFromInstructions

• Chart from Instruction File Information
  • Displays a chart summarizing data contained in files, as directed by an instruction file.

aBatchArchIntro

• Batch Architect Package Introduction Information
  • Provides facilities to coordinate the simulation of data and generate batch files for replicated analyses.

ContainedTreeSim

• Coalescence Simulated within Current Tree Information
  • Generates tree by a simple coalescence model of a neutral gene with constant population size, within species trees. Branch lengths are assigned according to generation of coalescence.The species tree used is a current tree found in a Tree Window or other tree context.

Coalescer

• Neutral Coalescence Information
  • Performs neutral coalescence within a population by a simple model of a neutral gene with constant population size.Remembers a tree of nodes, with branch lengths assigned according to generation of coalescence. The default population size is 10000.

ReconstructAssociation

• Reconstruct Deep Coalescence Information
  • Reconstructs a contained tree within a containing tree so as to minimize the amount of deep coalescence (failure of lineage sorting). The contained tree is assumed to be rooted.

aCoalescencePkgIntro

• Coalescence Package Introduction Information
  • Provides simulations and calculations for coalescence (genetic drift) within populations.

IncrementalConsenser

• Majority-Rule Consensus Information
  • Calculates the majority-rule consensus tree.
• Semistrict Consensus Information
  • Calculates the semistrict consensus tree.
• Strict Consensus Information
  • Calculates the strict consensus tree.

aConsensusIntro

• Consensus Trees Package Introduction Information
  • Calculations for consensus trees.

NumberFor2CharAndTree

• Pagel's 1994 test of correlated (discrete) character evolution Information
  • A statistical test, described in Pagel(1994), for nonindependent evolution of two discrete, binary characters

aCorrelPackageIntro

• Correl Package Information
  • Correl is a Mesquite package for examining character correlation.

TaxaDistFromMatrix

• Absolute Distance (General) Information
  • Absolute distance from a character matrix.
• F81 distance Information
  • F81 (Felsenstein, 1981) distance from a character matrix.
• F84 distance Information
  • F84 (Felsenstein, 1984) distance from a DNA matrix.
• Jukes Cantor distance Information
  • Jukes Cantor distance from a DNA matrix.
• K2P distance Information
  • K2P (Kimura 2-parameter) distance from a character matrix.
• Uncorrected (p) distance (DNA) Information
  • Uncorrected (p) distance from a DNA matrix.
• Uncorrected Distance (General) Information
  • Uncorrected distance from a character matrix.

TaxaDistanceSource

• Average of Several Distances Information
  • Average of several distances among taxa, e.g. average from several data matrices.

IncTaxaDistanceSource

• Distance of Contained Taxa Information
  • Distances among taxa according to distances among contained taxa (e.g., genes).
• Node Count (Speciation Patristic) Distances implied by Tree Information
  • Distances among taxa implied by counting nodes along branches of tree from one taxon to another (Speciation Patristic distances).
• Patristic Distances implied by Tree Information
  • Distances among taxa implied by path-length distance along branches of tree from one taxon to another (Patristic distances). Unassigned branches are treated as of length 1.0.
• Shared History Distances (Covariance matrix) from Tree Information
  • Distances among taxa implied by length of shared history (distance from root to most recent ancestor). This is the most common Covariance/Variance matrix used in GLS methods. Unassigned branches are treated as of length 1.0.
• Shared Proportion Distances implied by Tree Information
  • Distances among taxa implied by proportion of total branchlength (root to tip) that is shared (Shared Proportion distances). Unassigned branches are treated as of length 1.0.
• Distances from Character Matrix Information
  • Distances calculated from a character matrix.

TreeInferer

• Cluster Analysis Information
  • Supplies trees obtained from cluster analysis on distance matrices.
• Distance Analysis Information
  • Supplies trees resulting from a tree inference based upon distances.
• Invariants-based Tree Inference Information
  • Supplies trees resulting from a search for trees based upon invariants.
• Likelihood Tree Inference Information
  • Supplies trees resulting from a search for maximum likelihood trees.
• Tree Searchers (old arrangement) Information
  • Supplies trees resulting from tree searches.
• Other Tree Inference Information
  • Supplies trees resulting from other criteria.
• Parsimony Tree Inference Information
  • Supplies trees resulting from a search for most parsimonious trees.

TreeClusterer

• Single Linkage Information
  • Supplies trees obtained from Single Linkage clustering.
• UPGMA Information
  • Supplies trees obtained from UPGMA clustering.

NumberFor2Taxa

• Distance between taxa Information
  • Counts the difference between two taxa.

aDistanceIntro

• Distance Matrix Package Introduction Information
  • Calculates and provides utilities for distances matrices.

BiSSELikelihoodCalculator

• BiSSE Speciation/Extinction Likelihood Calculator Information
  • Calculates likelihood with a tree of a species diversification model whose speciation and extinction rates depend on the state of a binary character (BiSSE model, Maddison, Midford & Otto, 2007).

TreeCharSimulate

• BiSSE Trees & Characters Information
  • Generates tree by a speciation/extinction model in which a character controls rates of speciation/extinction. Time to next event drawn from negative exponential distribution.
• Evolving Speciation Rate (Continuous Character) Information
  • Generates tree by a speciation model in which the speciation rate evolves by a Brownian motion model.

DivCategCharMLCalculator

• BiSSE Net Diversification Likelihood (Calculator) Information
  • Calculates likelihood with a tree of a species diversification model whose rates (r = spec. - ext.; a = spec./ext.) depend on the state of a binary character (BiSSE model, Maddison, Midford & Otto, 2007).

SpecExtincMLCalculator

• Speciation/extinction Likelihood Calculator Information
  • Calculates likelihoods using a speciation/extinction model reduced from the BiSSE model (Maddison, Midford & Otto 2007)

aDiverseIntro

• Diverse Package Information
  • Diverse is a Mesquite package for examining speciation and extinction.

aDmanagerIntro

• DManager Package Introduction Information
  • Provides special tools for managing data and taxa.

aMBIntro

• MrBayes Package Introduction Information
  • Provides links to MrBayes analyses.

aMeristicIntro

• Meristic Data Package Introduction Information
  • Provides basic facilities for handling meristic characters.

AAProperty

• Kyte & Doolittle Hydrophobicity Information
  • Returns hydrophobicity of amino acid using the scale of Kyte, J & R.F. Doolittle (1982) J. Mol. Biol. 157:105-142. Numbers from http://www.whatislife.com/reader/protein/aa.html
• Amino Acid Molecular Weight Information
  • Returns molecular weight of amino acid

NumberForCharAndTaxon

• Amino Acid Properties Information
  • Returns property of amino acid
• GC Information
  • Returns 1 for G or C, 0 for A or T.
• Lower Case Information
  • Returns 1 if state symbol is a lower case letter.

CategDataSearcher

• BLAST in Web Browser Information
  • BLASTs selected data against GenBank.
• Top BLAST Matches Information
  • Does a BLAST search against GenBank on selected data and returns the top BLAST matches for each sequence selected.

FindSequenceCriterion

• Maintain Clipboard Match Information
  • Finds the first occurrence of the sequence in the clipboard, within a designated taxon, and maintains that match as the clipboard changes.
• Maintain Target Match Information
  • Finds the first occurrence of the sequence in the text area below the matrix, within a designated taxon, and maintains that match as the text area changes.

FindSequenceCriterionG

• Find Missing Information
  • Finds the next occurrence of missing data in a matrix of molecular data.
• Find Incomplete Codons Information
  • Finds the next occurrence of a partial codon triplet in a matrix of molecular data.
• Matching Sequence Information
  • Finds the next occurrence of a sequence in a matrix of molecular data. Allows a certain number of mismatches.

Blaster

• BLAST Local Server Information
  • BLASTs a database on the same computer as Mesquite.
• BLAST NCBI GenBank Server Information
  • BLASTs the NCBI GenBank server at NIH

aMolecIntro

• Molecular Utilities Package Introduction Information
  • Provides utilities for molecular data.

aOrnamentalIntro

• Ornamental Trees Package Introduction Information
  • Has extra methods for drawing and decorating trees.

PairMakerChars

• Most Pairs Information
  • Chooses taxon pairings regardless of contrast in a character, so as to maximize the number of pairs that are phylogenetically independent.
• Pairs Contrasting in State of One Character Information
  • Chooses taxon pairings so as to maximize the number of pairs that are phylogenetically independent, subject to the constraint that each pair shows a contrast the states of a binary character.
• Pairs Contrasting in State of Two Characters Information
  • Chooses taxon pairings so as to maximize the number of pairs that are phylogenetically independent, subject to the constraint that each pair shows a contrast the states of both of two binary characters.

aPairwiseIntro

• Pairwise Comparisons Package Introduction Information
  • Performs pairwise comparisons character correlation analyses.

Ordinator

• Canonical Variates Analysis Information
  • Performs canonical variates analysis on a continous-valued matrix.
• Evolutionary Principal Components Information
  • Performs Maddison and Dyreson's evolutionary principal components analysis on a continous-valued matrix.
• Principal Components Analysis Information
  • Performs principal components analysis on a continous-valued matrix.
• Among-group PCA Information
  • Performs among-group principal components analysis on a continous-valued matrix.
• Within-group PCA Information
  • Performs within-group principal components analysis on a continous-valued matrix.

OrdinationAssistant

• Display Character Loadings Information
  • Shows character loadings in ordination.

aRhetenorIntro

• Rhetenor Package Introduction Information
  • Multivariate analyses and morphometrics.

TreeSearcher

• Mesquite Heuristic (Add & rearrange) Information
  • Searches for optimal trees by adding taxa then rearranging the tree.

TreeSwapper

• NNI Rearranger Information
  • Rearranges a tree by nearest neighbor interchange (NNI). Does not handle trees with polytomies.
• SPR Rearranger Information
  • Rearranges a tree by subtree pruning and regrafting (SPR).

aSearchIntro

• Tree Search Package Introduction Information
  • Coordinates simple searches for optimal trees.

TaxonOnWebServer

• Catalogue of Life Information
  • Provides a URL to a taxon in the Catalogue of Life
• GenBank Taxon Information
  • Provides a URL to a taxon in NCBI GenBank
• Google Information
  • Provides a URL to a taxon in Google
• Tree of Life Web Project Information
  • Provides a URL to a taxon on the Tree of Life Web Project
• iSpecies Information
  • Provides a URL to a taxon in iSpecies
• uBio Information
  • Provides a URL to a taxon in uBio

aTolIntro

• Tree of Life Web Project Interface Package Introduction Information
  • Provides interfaces to the Tree of Life Web Project.

DetTreeModifier

• All Rerootings Information
  • Reroots tree at all nodes.
• Rearranged tree Information
  • Supplies trees that are rearrangments of a given tree. The original tree is NOT included among the rearrangements.

RndTreeModifier

• Augment Tree Randomly Information
  • Augments tree by random placement of excluded taxa. There are three modes: adding only to original branches, ignoring lengths; adding to any branch, considering branch length; adding to any branch, ignoring branch length. With lengths considered, probability of placing taxon on a branch is proportional to the branch's length.
• Add Noise to Branch Lengths Information
  • Adds noise to branch lengths of tree. Noise is Normally distributed, with variance as selected. By default the variance is be proportional to current branch length, so that if branch length is 10 and you've indicated a variance multiplier of 0.1, the noise added will have a variance of 1.0. Negative branch lengths are not allowed, and are changed to zero.
• Occasionally Randomly Modify Information
  • With specified probabililty, will ask random tree modifier to modify current tree.
• Random Branch Moves Information
  • Rearranges tree by random branch moves.
• Randomly Resolve Polytomies Information
  • Randomly resolves polytomies in tree. All possible resolutions are equiprobable. Thus, if the tree is a polytomous bush, the resulting resolved trees will be distributed equivalently to that from the Equiprobable Trees module.
• Rarefy Tree Information
  • Rarefies tree by randomly excluding taxa. If some taxa are selected, random exclusion is limited to the selected taxa.
• Reshuffle Terminal Taxa Information
  • Shuffles (permutes) the taxa among the terminal nodes.
• Randomly Rotate Nodes Information
  • Randomly rearranges the immediate descendants of each node; thus, it does not change the topology, just its appearance.

DistanceBetween2Trees

• Average Difference of Values Associated with Nodes Information
  • Calculates the average differences in values associated with nodes across those clades shared between two trees (excludes the clade consisting of all taxa).
• Patristic distance correlation Information
  • Calculates the product moment correlation coefficient among the off-diagonal elements of the patristic distances matrices of two trees. Ignores unassigned and negative values in the matrices. If employed as a distance, converts scores from 1 to -1 to scores from 0 to 2
• Fraction of Clades that are Shared Information
  • Calculates the fraction of the total number of clades in two trees that are shared between the trees (excludes the clade consisting of all taxa).
• Shared Clades Information
  • Calculates the number of shared clades between two trees (excludes the clade consisting of all taxa).
• Shared Partitions Information
  • Calculates the number of shared partitions between two trees. If used as a distance, then converted by subtracting shared partitions from the maximum possible, i.e. the number of partitions in the subtree of shared taxa in the tree with the most partitions.

TreeBlockListUtility

• Concatenate tree blocks Information
  • Concatenates selected tree blocks into a new tree block.
• Duplicate tree blocks Information
  • Duplicates selected tree blocks into a new tree block.

TreeUtility

• E-mail Tree Information
  • Calls mailto: to email a text image of the tree.
• Select Taxa in Same Clade Information
  • Selects all taxa that are descendants of the most recent common ancestor of the selected taxa.
• Reorder Taxa By Tree Information
  • Reorders taxa to match the order in the tree.
• Copy Newick Tree for Open Tree Information
  • This will copy a tree in Newick format to the clipboard ready to be uploaded into Open Tree (opentreeoflife.org). It will optionally convert node values such as consensus frequences as branch lengths (as that is one way Open Tree imports support values for branches).

aTreeFarmIntro

• Tree Farm Package Introduction Information
  • Extra utilities for trees, including comparisons, randomizations and manipulations.

aiTextIntro

• iText Information
  • iText is a package for saving PDF files within Mesquite.

aJamaIntro

• JAMA Introduction Information
  • Introduces the JAMA library.

aJSciIntro

• mesquite.jsci Package Introduction Information
  • Introduces the JSci library.

aPALIntro

• PAL Introduction Information
  • Introduces the PAL library.