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New Features and History of Changes

Here are some of the more notable new features and bug fixes since version 1.0. Bugs that could have yielded errors in substantive results (e.g. a bug in a phylogenetic calculation) are marked with .

Beginning with version 1.1, a list of new modules in the latest version can be seen by choosing "List new modules" from the Help menu.

There is also a short list of release dates.

Version 2.72

New Features

  • Parsimony analyses can now be done with meristic data matrices, using Linear Parsimony (analogous to Ordered parsimony with categorical data).
  • There is a new tree source, Concatenate Multiple Tree Sources, that brings together several tree sources into one.
  • New options have been provided for intepreting how information is attached to nodes and branches of trees, which affects how the information behaves when the tree is rerooted. Branch lengths are treated as if they belong to the branch ancestral to a node, and so when the tree is rerooted, the branch length is reassociated so as to continue to refer to the same branch between nodes. However, the name of a clade needs to remain associated with the same node regardless of rerooting. Ned Young pointed out that other information always behaves as if attached to the nodes (not the branches between nodes). We have changed the behaviour so that branch widths and branch color behave as if attached to the branch. We have also provided a function "Reinterpret Internal Node Labels", available in the Alter/Transform Tree submenu of the Tree menu of a Tree window. When this is selected you can change information associated with the tree as node labels and associate it with the nodes or branches in a different form. This can be useful, for instance, if you have imported a tree from MrBayes with posterior probabilities attached as node labels. Being attached as node labels, the probabilities will be mis-associated with nodes if the tree is rerooted. You can move the probabilities from node labels to numbers attached to branches using Reinterpret Internal Node Labels.
  • The reporting of crashes and checksum errors has been improved.

Bug Fixes

  • (substantive) When taxa were deleted, there was a chance that a crash would occur, and this crash could corrupt data. This crash occurred inconsistently, but if it did occur, then you would have received a warning that data might be corrupted. If you ignored the warning, then your character data or other information could have become associated with the wrong taxa. This bug has been fixed.
  • (substantive) When a 3 dimensional (i.e. multi-item) continuous character matrix was exported to a file, and in a few other contexts, the exported matrix would have the items written incorrectly. This did not affect typical continuous matrices, only those with multiple items in each cell of the matrix. This bug has been fixed.
  • Reading and writing of DNA matrices was fixed so that it preserved lower case symbols
  • Trees exported to PHYLIP and other formats are now written without "decorations" such as branch colors, which tended to render the trees unreadable by other programs
  • Sorting of columns now respects numerical order (and thus 2.0 is sorted as between 1.0 and 10.0)
  • Various small bugs were fixed.

Version 2.71

New Features

  • The crash reporting system now invites you to enter an email address so that the Mesquite developers can contact you if we need more information to diagnose or fix a problem. Entering an email address is optional.
  • A new scripting command, getValuesTabbed, can be sent to chart windows to obtain the chart values as a simple list of numbers separated by tabs.

Bug Fixes

  • Various small bugs were fixed.

Version 2.7

New Features

  • There is a new crash reporting system that can send reports to the Mesquite development team. When certain crashes occur, a dialog box will appear offering to send a report. We urge you to permit the report to be sent; it will help us fix bugs.
  • Speed and memory use has been improved considerably for large matrices and trees. This permits many more taxa and characters to be conveniently handled.
  • Consistency Index and Retention Index can be calculated for trees with individual characters and with matrices. These are available in various places, for instance in the List of Characters Window, Column>Number for Character>Character Value with current tree...
  • NEXUS tree files without translation tables can now be read directly, without first reading or making the corresponding taxa block.
  • The BiSSE simulation of trees and characters (available through Trees & Diversification Characters in the Taxa & Trees menu) now asks in the simulating dialog box what prior probability to put on state 1 at the root. The default is to use the equilibrium (stationary) frequencies as the prior, but you can enter 0.0 to indicate the state at the root is necessarily 0, 1.0 to indicate it is necessarily 1.
  • Tree simulations normally are set to be repeatable; i.e. if you ask for tree 1 several times, you will get the same tree 1. This can now be turned off by deselecting the menu item Simulation Repeatable. This could be useful in scripting under different scenarios to ensure each scenario uses an independent random number sequence.
  • There is a new tree window tool, Node Age Constraints (shaped like an anchor), that permits age constraints to be assigned to nodes. These constraints are not yet used by any standard Mesquite module, but could be used by optional modules. More details are given here.
  • The function to save trees to a file without holding them in memory, previously available under File>Export as "Export NEXUS Tree File from Tree Source" has been moved to Taxa&Trees>Save Trees To File from.
  • A new source of trees is Concatenate 2 Tree Sources, which supplies trees from two separate sources as if they were one source. Trees from the first source have an attached value of "1", while trees from the second source have an attached value of "2". Concatenating tree sources can be useful for example to concatenate two tree files that are too large to read into memory at once. More details are given here.
  • There is a Revert To Saved menu item in the File menu that reverts the project to its last saved state. Choosing this menu item is the equivalent of closing the file without saving, and then rereading it from disk. If you have linked files open, then choosing it is equivalent to closing all files in the project without saving, and then rereading the home file of the project from disk.
  • There is a new submenu, "Tree Inference", in the Taxa&Trees menu, that shows functions to infer phylogenetic trees. Currently the only built-in tree inference methods are Mesquite's heuristic Add & Rearrange, and simple Cluster Analysis. However, we anticipate that optional packages will soon be released to add functions.
  • The Tree Window has a new scripting command, getAsTable, that returns a string in the form of a table that can be converted into a tab delimited table. It summarizes ongoing calculations on the tree such as traced characters and values at nodes. The format is "Calculation Type<tab>node value<tab>node value<tab>...".
  • Character matrices can be marked as "hidden", which means that they will not be included in most menus and dialog boxes in which you can choose matrices, and they will not appear in the project panel at the left of the window. To set the visibility, go to the List of Character Matrices, Column>Visibility of Matrix. Once the column appears, select the rows for the matrices whose visiblity you want to change, and choose Toggle Visibility from the drop down menu at the top of the column.
  • You can now suppress decorations on taxon names in the tree window (e.g. the "*" that indicates a footnote is available) by deselecting Show Footnotes Etc. under Taxon Names in the Drawing window.
  • The tree window now has a menu item, Legends to Default Positions, that can recover legends that have become lost off screen.
  • The Square Tree drawing form now has a Corners submenu that permits drawing with rounded corners:

  • You can assign a name to your project other than the name of the home file. The project name is then displayed on the window's title bar. To change the name of the project, touch on "Project" near the top of the project panel at the left of the window. In the drop down menu, choose the menu item Name of Project...
  • When a duplicate taxa block is read, for instance in a linked file, the first taxa block is not reordered. (Actually, it is reordered temporarily to complete reading of the linked file, but then reverted to the original order.)
  • Mesquite now requests more memory by default.
  • Mesquite's phone home system now sends the following information to the Mesquite server when you start up Mesquite: your IP address, your operating system, and your version of Java. (Similar information is sent to any web server you visit when you browse the web.) This is sent so that we can better prioritize what operating systems and Java versions to support. If you want to turn this reporting off, deselect "Check for Notices on Mesquite Server" from the Defaults submenu of the File menu.
  • With a character matrix open, you can now quickly remove all invariant characters by choosing Remove Invariant Characters from the Alter/Transform menu of the Matrix menu.
  • The Merge Taxa command now allows you some control over how the name of the merged taxon is formed.

Bug Fixes

  • (substantive) There was a bug that could scramble the Taxa Associations used to indicate how taxa in one taxa block are associated with taxa in another block (e.g., for genes in species). Scrambling could occur if taxa were reordered then new taxa added, and would result in the wrong taxa being listed as associated. This bug has been fixed.
  • (substantive) There was a bug that could place incorrect data into a continuous valued character matrix if a section was cut, and then Undo called. The error would have likely been obvious. This bug has been fixed.
  • (substantive) There was a bug that caused Mesquite to misinterpret typed character states when editing a character matrix that used certain non-standard lists of symbols. This would have generated a warning about checksum errors. This bug has been fixed.
  • (substantive) The Translate DNA to Protein feature had a bug in that it on occasion removed the last amino acid; this has been fixed.
  • Trace Character over Trees could sometimes display the incorrect character name when characters were excluded. This bug has been fixed.
  • The BiSSE viewer would record the wrong character number into a file when saved, so that when reopened the file would disply statistics based on a different character than it had previously. This is fixed.
  • We have fixed a bug that would cause Mesquite to issue an unnecessary warning that the log file could not be written.
  • There was a bug in the Undo system when a cell of a character matrix was being edited; repeated requests to Undo could place unexpected states into the cell. This is fixed.
  • Some bugs with tree window scrolling, introduced in version 2.6, have been fixed.
  • Various other small bugs were fixed.

Version 2.6

New Features

  • There is a new interface simplification system.
  • There is a new system for installing updates for Mesquite and extra packages. If an update is available, you will be notified when Mesquite starts up. Updates that you choose not to install will still be available via File>Available to Install or Update.
  • The Tree Window's automatic sizing of the tree drawing has been improved, and the menu items controlling tree sizing have changed.
  • You can now display boolean values for characters in the information strip at the top of the data matrix, using the Matrix>Add Info Strip>Boolean Info Strip submenu. The two initial booleans whose values you can display in this way are whether or not the character has two or more states, and whether or not it is included. You can remove the information strip by choosing Remove Info Strip in the menu you get when you touch on the info strip.
  • You can now export distance matrices from various sources (patristic distances, pairwise sequence distances, geographic distances) to a text file. This can be done by selecting Export from the File menu, and choosing "Export Taxa Distance Matrix".
  • Mesquite can now read treefiles produced by BEST (Bayesian Estimation of the Species Tree), the program by Liang Liu.
  • The menu items for Summarize State Changes Over Trees and Summarize Changes In Selected Clade have been moved to the Analysis menu
  • The "phone home" system by which Mesquite checks its website to notify you of updates now tells the server which version of Mesquite you are using. Mesquite does not transmit any other data about you, except what your web browser does when you go to a website. (You can disable the "phone home" system in the Defaults submenu of the Edit menu.)

Bug Fixes

  • (substantive) If consensus trees were constructed over trees with branch lengths stored, the average branch lengths of the terminal branches of the consensus tree was incorrect. This has been corrected.
  • (substantive) If new characters or taxa were inserted in an existing matrix or taxa block anywhere but in last position, then subsequent characters or taxa may have had their status in selection sets corrupted. This would not directly lead to a substantive error, but could indirectly if those selection sets were subsequently used for manipulating data. This has been fixed.
  • (substantive) If new characters or taxa were inserted in an existing matrix, for example by importing FASTA files, then subsequent use of the manual alignment tools (e.g., the multiple sequence splitter) might in rare circumstances cause loss of a few bases from the ends of sequences. As far as we know, Mesquite would have given a warning if this happened. (Thanks to Jolanta Miadlikowksa for reporting this.)
  • Mesquite can now more successfully import and export PHYLIP files.
  • Undoing some operations in the data matrix caused Mesquite to crash. This has been fixed, but only by preventing the ability to undo some actions that could lead to changes in the entire matrix if the matrix is very large. You can set the maximum size of the matrix that is fully undoable using File>Defaults>Matrix Limits for Undo...
  • INTERLEAVED NEXUS files with more than 2000 characters per interleaved block were written incorrectly by Mesquite; this has been fixed. (Thanks to Jolanta Miadlikowksa and Johan Nylander for reporting this.)
  • Moving multiple sequences in Mesquite using the "Splits multiple sequences" tool was very slow; this has been fixed.
  • Shift to Match Other was not finding many sequences that matched that were matches; it is now much improved.
  • Missing data in FASTA files is now correctly written.
  • Various other small bugs were fixed

Version 2.5

New Features

  • The default appearance of Mesquite's windows have changed. You can alter the general colors used by choosing items from the File>Defaults>Color Theme menu.
  • Consensus tree calculations are now available in the standard Mesquite packages (there are separate consensus tree calculations in the TreeSetViz package). Strict, semistrict, and majority rules consensus are available.
  • Results of calculations over multiple trees in the Tree Window are available without scripting through the new Step through Trees feature.
  • Mesquite's parsimony ancestral state reconstructions can now examine individual Most Parsimonious Reconstructions (MPRs), and calculate how many there are.
  • There are two Summarize State Changes Over Trees modes, both of which summarize the frequencies of each sort of character change (e.g., from state 0 to state 1) based upon character histories reconstructed over each of a collection of trees.
  • There is a new Project Panel at the left of most windows to help you keep track of your data objects such as taxa blocks, character matrices and tree blocks. With it you can display, export, rename, or delete these objects.
  • The Tree Window has a new Tree Info Panel, available by touching the blue "i" () in the tree window. This panel shows basic information about the tree and its notes. It also has a Values section in which you can display values from various calculations (character likelihood, etc.).
  • Selection of taxa and branches in the Tree Window has been changed to be more natural, using the standard arrow cursor via clicking and dragging.
  • The Character Matrix editor has various improvements:
    • There is a Matrix Info Panel, available by touching the blue "i" () in the matrix editor window. This panel shows basic information about the matrix and its entries. For categorical matrices, you can edit character names and character state names; for sequence matrices you can edit a comment for the particular esquence; for continuous matrices you can adjust the matrix's items and their names.
    • Copy/paste of molecular sequences have been improved.
    • Character names can be written diagonally for categorical and continuous matrices.
    • You can now change the symbols used for missing data and inapplicable (gaps) using Matrix>Current Matrix>Missing Data Symbol and Matrix>Current Matrix>Inapplicable Symbol
    • For DNA or RNA sequence data, there is a new feature to alter data (available in the Matrix>Alter/Tranform>Convert to RY that converts A or G to R, and C or T to Y.
  • There are two new tools for manual sequence alignment. These are described in the Align manual:
    • Selected Block Mover
    • MultiBlock Splitter
  • There is a new data type, meristic, for counts (number of teeth, etc.). This is not widely supported in analyses, and has been introduced now for several internal bookkeeping functions.
  • The boxes for taxon names and character names in the Character Matrix Editor are now colored independently from the internal cells of the matrix. These have their own submenus in the Matrix menu to control them.
  • The Tree Legend has been renamed as "Values for Current Tree". Its functions are also duplicated in the Tree Info Panel "values" section.
  • By default menu items and dialog boxes show all choices, not just the primary choices.
  • The tree drawing menu has been reorganized to put Taxon Names Angle under Names.
  • Select taxa through search of taxon names. This feature allows you to select taxa if a portion of their names match the specified text. It is available from the Select>Select Taxa submenu in the character matrix editer, or in List>Select Taxa submenu in the List of Taxa window.
  • There is a new module to calculate the average tree depth, that is, the average length of the paths between terminal taxa and the root, called "Average Tree Depth".
  • Export NEXUS Tree File from Tree Source. This feature allows you to save a text file directly from a tree source.

Bug Fixes

  • (substantive) The correlation analysis using pairwise comparisons occasionally would display results that were not complete (not based on a full sample of pairings).
  • (substantive) When taxa were added, deleted or reordered, some special information such as branch widths, colors and notes associated with the nodes of trees became associated to the wrong nodes. Branch lengths were not affected by this.
  • (substantive) Simulations of tree and character evolution simultaneously using "BiSSE Trees & Characters" (available via Trees & Diversification Characters menu item in Taxa & Trees) in some circumstances would have been done using parameters different from those specified in the dialog box, depending on the sequence with which parameters were specified.
  • Hennig86/NONA file export had incorrectly counted comments. Hennig86/NONA file export now writes CCODE specifications explicitly, not assuming a default.
  • The autotab feature to the quick key selector tool now works correctly in the data editor.
  • Many other smaller bugs were fixed.

Version 2.01

New Features

  • "Phone home" system. Mesquite now checks its website on startup to see if there are notices for users, for instance about updates or bugs. (This can be disabled in the Defaults submenu of the Edit menu.) Other packages can also be set to check their websites. This checking does not transmit data about you other than what your web browser does when you go to a website.
  • The search facility to help you find features ("Search Features", available in each window: ) has been improved to include menu items and tools in open windows.
  • To help minimize user confusion, there are new options in how Mesquite by default presents choices of modules to the user. First, dialog boxes that offer a choice of module may now show more detailed choices. For instance, whereas previously you would be offered a choice "Tree value using character", now there will also be a list beneath it of the particular values available:
    This new default can be reverted to the old style by deselecting "Show Subchoices in Module Dialogs" in the Defaults submenu. Second, calculations that use characters or matrices can be set to use Stored Characters and Stored Matrices by default, without asking. This default may help novice users who otherwise would be confused by a request about simulations and so on. You can set this default as explained on the Characters page.
  • The Defaults menu is now a submenu of the File menu, and is available from all windows.
  • GenBank and GenPept import. Mesquite can now import GenBank and GenPept files. If multiple files are dropped onto a molecular matrix of the same sort (e.g., DNA), then these sequences will be added to the matrix.
  • Drag and drop of sequence files. You can now drag a collection of FASTA, NBRF, or GenBank files and drop them onto an existing molecular matrix. Mesquite will ask you to specify the file format, and then it will read in the sequences and append them to the bottom of hte matrix
  • New alignment tools (in the Align package):
    • Align DNA to Protein. A DNA matrix can be aligned to match that of a translated amino acid alignment.
    • Muscle Align. A portion of a sequence matrix can be sent to MUSCLE to be aligned and then reimported back into the matrix.
    • Shift to Minimize Stop Codons. Sequences will individually be shifted 0, 1, or 2 based to minimize the number of stop codons in each sequence. This is useful to set the reading frame of each sequence, for example for subsequent translation to amino acids.
  • Tree of Life Web Project linking and other online databases. Trees from the Tree of Life Web Project can be downloaded and navigated. In addition, a new tool in the tree window will search for taxon names in various on-line databases, including TreeBase, iSpecies, etc.
  • Export NEXUS Tree File. This new exporter allows you to save a tree file (optionally including a taxa block) from a Mesquite project.
  • A Search Within Clade Tool is available in the tree window. This tool rearranges the branches above the node touched looking for a better tree. The objective function used (e.g., treelength, or something else) can be chosen by the user. This is similar to MacClade's search tool in that it directly rearranges the current tree.
  • Randomly Resolve Polytomies has a new convention. In previous versions it paid little attention to branch lengths, simply using the same convention as when a user moves branches. This resulted in the descendant nodes acquiring different distances from the root than they had had before resolution. The new convention is to preserve distance from root when resolving polytomies. The user however must specify what portion of branch lengths to put on new branches formed during the resolution.
  • The Contained Associates tree drawer, most commonly used to display gene trees within species trees, has been renamed as Contained Gene (or Other) Trees.
  • The Defaults menu of the Log window has been moved to a submenu of the File menu, and is now available in all windows.

Bug Fixes

  • Various bugs concerning behavior of windows and dialogs under Linux and Mac OS X were fixed.
  • () Deep coalescences were miscounted if a species or population lacked any containing genes. Such a species or population would contribute -1 to the deep coalescence count in such a circumstance (it should have contributed 0). This could, for instance, result in a deep coalescence score of a negative number, but it could also simply lower the total. This bug did not affect relative scores among trees (as long as they contained the same set of populations and genes) and so many analyses, such as searching for optimal species trees, would be unaffected. This bug was fixed in build j28 of version 2.01. The very first build of 2.01, j27, released for a few hours, has this bug.
  • () The Number of Stops in a taxon in some circumstances was underestimated if there were some characters whose codon positions were not specified.

Version 2.0

New Features

  • Search system — A "Search" text entry box is now available at the top of most windows (in the Log window, at the bottom). Enter text there and hit Return, and the text will be sought. There are several modes, marked by different symbols:
    • & — Search Features, AND: searches through information about Mesquite's features and returns a description of those features matching ALL of the search terms
    • / — Search Features, OR: searches through information about Mesquite's features and returns a description of those features matching ANY of the search terms
    • d — Search Data: searches the current data file or project and returns objects (e.g. taxa, characters, sequences) that match the search string.
    You can choose the mode by touching on the symbol until the desired mode appears. In the Search Features modes, the results also give indication as to how the feature might be accessed. (There may even be a Try It! link that offers to invoke the feature.)
  • New windowing system — By default, all of the windows of a single project now appear as tabbed panels within a single window. This change was made to limit window proliferation. If you want to "pop out" a tab to be a separate window, hit the curved arrow button within the tab (you can "pop in" the window again using the curved arrow button at the upper left side of the separated window). You can revert to the old system of many windows using the Open Windows as Tabs item in the Defaults submenu of the File menu.
  • Wizard-style dialogs — In many contexts Mesquite needs to ask a series of questions when a feature is requested. In previous versions these would appear as a series of dialog boxes; in version 2 these now appear as a single dialog that moves from one question to another, in the style of a wizard. This change was made to make an area in the dialog to give a more thorough explanation of the request, and to minimize the visual distraction of changing dialog sizes. You can revert to the old style of separate dialog boxes (which may work better on some operating systems) using the Use Wizard-style Dialogs item of the Defaults submenu of the File menu.
  • Diverse package — There is a new package of modules that estimates and simulates models of speciation and extinction. Some of its features are:
    • Estimating speciation/extinction rates
    • Detecting state-dependent differential speciation/extinction (BiSSE)
    • Birth/Death tree simulation
    • Simulations with evolving characters that affect speciation/extinction
    • Lineages through time plots
  • Coalescence simulation with migration — Coalescence within a population/species tree can now be simulated with a selected rate of migration per generation among populations.
  • Trace Character Over Trees — This feature has been improved in several ways. The fraction of trees without a node is now shown, as is the fraction of trees with the node but not counted as they have ambiguous state assignment (by whatever criteria are chosen). The states at the terminal taxa are now shown. There is a new calculation mode, Average Frequencies Across Trees, available if the ancestral state reconstruction module yields frequencies or probabilities; this calculates, for each state, the average frequency across all trees (including trees in which the frequency for that state is very low or zero).
  • Sample Trees Directly from File (now called Sample Trees from Separate File) — One can choose as a source of trees a random subsample of the trees contained within a treefile.
  • Undo — You can now undo some changes you might make to the character matrix in the character matrix window. In particular, edits of an individual cell, or changes made by the items in the Matrix>Alter/Transform menu, are now undoable. Other changes (e.g., deleting a character) are not yet undoable.
  • Consensus sequences — One or more consensus sequences can be displayed in the character matrix editor.
  • Adding sequences to an existing matrix — FASTA or NBRF files dropped onto a matrix of DNA or protein sequences can be read in and appended to those matrices.
  • Fusing genes to single matrix — In concatenating matrices, you can now contatenate matrices with different sets of taxa, facilitating fusion of different genes into a single matrix
  • Alternative naming schemes for taxa — This feature was introduced in version 1.1 as "Archived names". It has been expanded to permit multiple archived naming schemes.
  • Matrix coloring to aid manual sequence alignment — There are two new Color Cells options that aid with manual alignment. One ("Aligning Colors") uses colors that emphasize purine-pyrimidine differences; the other highlights sections that appear to be slightly misaligned.
  • Various other smaller improvements have been made, for instance you can now import a PHYLIP tree file directly (without having to establish a taxa block first), and you can choose darker colors when assigning colors to objects.

Bug Fixes

  • () There was a bug in writing decimal numbers as strings. Frequently, the 7th or 8th significant decimal place of a number would be written incorrectly. This did not affect how data were stored in the file; it affected only the reporting of results and screen display. This is unlikely to have a serious effect on published results for two reasons. First, it usually affected only the 7th or 8th significant decimal place. Second, the situations in which it affected a more important decimal place were obscure and perhaps rarely used by users. These are: Density output in Scattergram; Parameters Explorer for newer likelihood calculations; Location of changes in Stochastic Character Mapping. In these cases, the 3rd or 4th decimal place could be affected. This bug has been fixed.
  • () On Windows operating systems, pasting into the data matrix often resulted in the loss of the first character of some rows. This may have been benign, but occasionally would result in data being pasted incorrectly (e.g. 1.234 received as 0.234). This bug has been fixed.
  • () Among the coalescence calculations, the method to resolve a polytomous contained gene tree failed to resolve all polytomies needed, leaving some unresolved. This resulted in inflated Deep Coalescence counts. This bug has been fixed.
  • () Fixed bug in which parsimony step matrix would be incorrectly written and could not be re-read properly if it refered to characters with more than 10 states.
  • Fixed bug in which Recode dialog box would disappear unexpectedly.


Version 1.12

Bug Fixes

  • () In versions 1.1 and 1.11 of Mesquite several of the simulations and randomizations had a bug in choosing the random number seed for the first item simulated or the first randomization. The designed behavior is for the simulations to begin with a random number seed based on the current clock, and then from that calculate base seeds for each of the replicates using the procedure described below under version 1.1 bug fixes. Version 1.12 has been corrected to use this designed behavior. However, in 1.1 and 1.11 for several of the simulations the first replicate always used 1 as its random number seed, although all subsequent replicates used the correct method as designed. This bug did not affect independence of replicates within a simulation of multiple replicates (except when multiple tree blocks were simulated using "Simulated Tree Blocks"), but it did affect independence among separate simulations/randomizations. Since the bug affected only the first replicate, it would not be expected to affect significance values unless very few replicates were used. The affected simulations/randomizations are: Simulated Trees (first tree used seed 1 always); Simulated Tree Blocks (first tree of each block used seed 1 always); Randomly Modify Trees (first tree used seed 1 always); Randomly Modify Matrices (first matrix used seed 1 always).
  • () When taxa are selected by the user and Rarefy Tree is used to generate trees with a requested number of taxa randomly deleted, taxa are chosen for deletion randomly only from among those currently selected. In previous versions of Mesquite this did not work correctly, in that frequently fewer than the requested number of taxa were deleted. This may have been evident to the user because the modified tree would have contained more taxa than expected. This bug is fixed in 1.12.
  • () The likelihood calculations for categorical characters were designed only for characters with a contiguous series of states starting at 0, and to prohibit other characters. That is, a character with states 0, 1, 2 would be permitted, but a character with states 1 and 2, or a character with states 0 and 2, would not be permitted. This requirement was mentioned in the manual, but the requirement was not enforced properly within the program, and thus Mesquite permitted the calculations with some such characters. The reconstructions are incorrect. In version 1.12 the prohibition is correctly in place; Mesquite will refuse to calculate likelihoods with such characters.
  • () A single character matrix can be modified from various windows, such as the List of Characters window (e.g., by moving, deleting characters) and the Character Matrix Editor. When a character matrix editor is open and a cell is being edited, the editing field could sometimes be misapplied to the wrong character or taxon if elsewhere characters or taxa are deleted, added or changed in order. The effect of this is that the state of one character or taxon can get copied inadvertantly to another character or taxon. This bug has been fixed.
  • A bug in the shading of character states for Trace Character History for continuous characters has been fixed. In previous versions there were situations in which a branch was given a color slightly offset from its correct color according to the legend and its state value. (The correct state could always be seen, however, by holding the cursor over the branch.) This has been fixed.
  • Fixed bug in Find Sequence (Matching sequence).



Version 1.11

Bug Fixes

  • () In previous versions of Mesquite, a Taxa Association between taxa blocks, for example one which records what haplotypes belong to what species, could come to have incorrect linkings if taxa were reordered in the file. This is not directly a substantive bug, but could yield calculations with errors if the user does not notice that taxa have become mis-associated. This bug has been fixed
  • Clustal Align now works under Windows
  • Various other small bugs were fixed.

Version 1.1

18 May 2006

New Features

  • Character evolution
  • Gene tree/species trees
  • Alignment (see the Align Package manual)
    • Manual alignment tools in editor (Block Mover, Sequence Pusher)
    • Automated pairwise alignment tool in editor
    • Submission of a selected region in the matrix to be aligned by ClustalW and then reincorporation of the newly aligned region into the matrix
  • Genetic Codes
    • Assignment of genetic codes to individual characters
    • Translation of nucleotide data to protein data
  • Molecular Data
  • Distances
    • Jukes-Cantor, Felsenstein 81, Kimura 2-Parameter, Felsenstein 84 distances
    • Great Circle distances in the separately-released Cartographer package
  • Charts
    • Values for Taxon Pairs now available in Bar & Line Charts and Scattergrams, allowing one to plot, for example, uncorrected distance versus corrected distance for all taxon pairs within a matrix.
    • Line charts
    • Bar & Line charts can now show cumulative results in various fashions (e.g., cumulative, cumulative average, reverse cumulative average)
  • Interactions with GenBank
    • Import into matrix the top BLAST matches to sequences selected in matrix
  • Interaction with MrBayes
    • live updating of trees produced by ongoing MrBayes analysis
    • exporter that merges matrices and includes a MrBayes block summarizing the partitions in the resulting matrix. Merged matrix can be mixed (DNA, protein, and morphological) using MrBayes's modified NEXUS format.
  • Managing matrices and files
    • fuse matrices into a single matrix, even if matrices refer to different taxon names (e.g., sequences of different genes), using a table of correspondences among taxa blocks
    • alternative taxon names (permitting you to have alternative naming schemes for taxa in a file)
    • include taxa from NEXUS, NBRF or FASTA files into current file, e.g. to add newly acquired sequences to an existing matrix
    • import/export Phylip tree files
  • Randomization (reshuffling) of matrices can now respect taxa partitions; also can reshuffle within taxa
  • PDF file saving of graphics of trees and other windows
  • Colors of character tracings can now be changed
  • Simplified installation process for Windows computers
  • A complete list of standard modules has been added to the manual.

Bug Fixes

  • () In previous versions of Mesquite, simulations and randomizations of trees and characters used a shortcut to go to the n'th replicate, cycling the (pseudo-)random number generator n times before entering the replicate. This caused adjacent replicates to be not entirely independent. In most cases we expect this bug would not have had a biasing effect if sample sizes were large. This bug has been fixed by adding 1 to the random number seed after cycling n times to generate independent random number sequences for each replicate.
  • Various bugs and inefficiencies affect memory use have been solved in file reading, tree display and printing
  • There were some copy/paste bugs, especially under Windows, that have been fixed
  • Swapping in heuristic tree search now retains only unique trees
  • NEXUS files with high-ASCII characters (e.g., letters with accents) are better handled
  • Various other minor bugs and inefficiencies have been fixed
  • build h61 (released 23 May 2006) has a few extra bugs fixed: (1) Categorical likelihood calculations no longer complain if root has zero length; (2) Bug in Java 1.5 on Mac OS X caused list dialogs not to respond properly to clicking "Show Secondary Choices"; workaround implemented; (3) Incompatibility with PDAP file exporter solved; (4) directory choice dialog under Mac OS X improved.

Version 1.06

New Features

  • The window showing annotatons for taxa, characters and cells of a matrix has been integrated into the Character Matrix Editor as a panel within that window. This makes it easier to annotate without having to manipulate two windows. This panel can be requested by the Show Annotations Panel item in the Matrix menu, or by touching on the small button () near the lower left of the Matrix Editor (beneath the taxon names). The pencil tool () has disappeared. Another change is that images in annotations can now be remote (i.e. URL's). Also, the annotations panel is also available in the List of Taxa window (for annotating taxa) and the List of Characters window (for annotating characters). In the list windows, the panel can be requested by touching on the small button () at lower left of the table.
  • Annotations can now be attached to the states of a categorical character, within the State Names Editor (available from the Matrix menu of the Character Matrix Editor). The annotations can be viewed by choosing Show State Annotations in the State_Names menu or by touching on the small button at lower left of the table ().
  • A legend is now available for the colors in a Character Matrix Editor. The legend can be shown by selecting Show Color Legend in the Matrix menu, or by touching the small button() at lower left of the Matrix Editor (beneath the taxon names). If you double click on a color in the matrix, the editor will move to a cell with that color.
  • There are buttons at the lower left of the Character Matrix Editor to open the List of Characters window () and the List of Taxa window (). Reciprocally, the List of Characters window has a button () to show the Character Matrix Editor.
  • Character matrices can now be viewed in a "Birds-eye view" with very narrow columns.
  • There is a State Names Strip available for categorical matrices under the Matrix menu. This shows a strip along the bottom of the matrix in which the names of characters and states are shown. Similarly when Bird's Eye View is used for a matrix, a Bird's Eye Closeup Strip appears below the matrix so that you can more clearly see the states of the characters of focus. Both of these strips can be made higher by going to their upper edges, clicking and dragging upward.
  • You can now view a character matrix in more than one window, by requesting an Extra Matrix Editor from the Characters menu. This is useful, for instance, if you want to have the cells of the two matrices colored differently.
  • The order of characters can now be managed through stored character orders. A Default Order of characters is automatically stored as characters are created. This default order is visible in the List of Characters window as the first column. If the order of characters is accidentally or intentionally changed (for instance using the Sort Tool) then the default order can be recovered easily by applying the Sort Tool to the Default Order column of the List of Characters window. In addition, you can store and reload other character orderings by showing the Stored Character Order in the List of Characters window (Columns menu). You can store the current ordering and recover previously stored orderings using the drop down menu from the Stored Order column heading. When you do this, you will see the numbers in the column change, but the characters will not immediately be reordered. The reason for this is that what is stored and displayed is simply a number for each character marking its position. It is up to you to use that ordering to resort the characters. Thus, to recover a former sequence of characters, load the stored ordering, then touch on its column with the sort tool.
  • There are new facilities for searching for sequences in molecular data files. Thes are found in the Edit menu for editor windows of molecular sequence data. These are:
    • Copy Sequence (at bottom of Edit menu): This copies the selected cells of the matrix into the computer's clipboard as a sequence. That is, whereas the standard Copy would place into the clipboard selected pieces of the matrix in tab-delimited text format (e.g., if the sequence AATCA is selected, "A-tab-A-tab-T-tab-C-tab-A" would be copied), this modified Copy Sequence command does not include tabs (thus, "AATCA" would be copied). This style of copying is useful when interacting with programs like Sequencher (TM). For instance, if you want to find a piece of sequence in a matrix in Mesquite within a chromatogram viewer of Sequencher, do the following: select the sequence in Mesquite, choose Copy Sequence, then go to Sequencher, select Find Bases, and paste the sequence as the search string.
    • Maintain Target Match (in the Find Sequence submenu of the Edit menu): This highlights and maintains highlighted the first occurence of a given sequence in a given taxon. First, you are asked which taxon to search in. Then, it displays a panel like this:

      underneath the matrix. The first button (red X) is to close the panel; the second pauses the search; the third allows you to select another taxon as your focus. If you type a sequence into the text area, the matching sequence (if any) will be highlighted in the matrix. Mesquite is constantly monitoring this text, and so you don't need to give any command to find again if you change the text. This is useful if working with a program like Sequencher. If you see a stretch of sequence while viewing chromatograms that you'd like to find in the matrix in Mesquite, type in the sequence into the text box and you will quickly be taken to it in the taxon.
    • Maintain Clipboard Match (in the Find Sequence submenu of the Edit menu): This is similar to Maintain Target Match, except that it obtains the search string not from the text area but from the clipboard. If the clipboard changes, the function will automatically find the sequence again in the matrix. This is useful if working with a program like Sequencher. If you turn on Maintain Clipboard Match, then you can copy stretches of a sequence within Sequencher, and Mesquite will automatically highlight it, without your having to return to Mesquite or give any other command to it. (Mesquite is constantly monitoring the clipboard to see if it changes).
  • There is an optional system for assigning and maintaining ID strings to uniquely identify taxa and characters. This can be turned on via the menu items Invent Unique IDs for New Taxa and Invent Unique IDs for New Characters in the Defaults submenu of the File menu. When enabled, newly created characters and taxa are automatically assigned IDs which are maintained even if the taxa or characters are rearranged through reordering, additions or deletions. These unique IDs are little-used in Mesquite at present, but eventually will permit users to reassociate taxa and characters from different files even after names have been changed (for instance, to re-read a tree file saved with different taxon names). The IDs will also be used in database connectivity and collaborative features. To assign IDs to already-created taxa or characters, go to the List of Taxa or List of Characters windows and choose Unique IDs from the Columns menu. IDs can be generated using the drop down menu from the column's header. The one disadvantage of assigning IDs is that the IDs are stored in the Taxa block and Characters block of the NEXUS file, which causes some programs to refuse to read the file. (PAUP* by default will refuse to read these files, but you can request that PAUP* ignore these extra commands by the command "set errorstop = no;" which is available in its Options Menu, Warnings and Errors.)
  • There has been a shift in NEXUS file format for annotations — the AN command is now used. This, unfortunately, produces files that are not readable by version 1.05. The reason for this change is to minimize text in the file when dealing with a large matrix with thousands of annotations.
  • Pairwise comparisons were previously forced to find all possible pairs. Users can now impose a limit so that only the first n pairs are found and considered. This is important if there are too many pairs to efficiently consider.
  • Support for the new Cartographer package.
  • Groups of characters and taxa can now be assigned grayscale values instead of just colors.
  • Rarefy Tree (a random tree modifier) now uses taxon selection. If some of the taxa are selected, than Rarefy Tree chooses which taxa to exclude randomly only from among the selected taxa.
  • There is a new option to export files, Old-Fashioned NEXUS, for use by programs that understand only a small subset of the NEXUS format such as MrBayes.
  • Trees can be drawn in "Eurogram" style by using Square Tree and selecting the menu item Cut Corners.
  • The Developer's documentation has been updated

Bug fixes

  • () Fixed bug that caused labels for internal nodes (including Bayesian support values) to be scrambled if the branch interchange or reroot tool was used.
  • () The PAUPConstraintTestParsimony template included with Batch Architecture for doing the test of monophyly has one of the searches incorrectly searching for the optimal trees with the converse of the constraint rather than the constraint itself; this has been fixed.
  • () Fixed bug that caused tree statistics to be displayed incorrectly in columns in the List of Trees window if trees were deleted.
  • Fixed bug in dialog boxes with lists from which to choose that made them unusable under Mac OS X 10.4.
  • Fixed bug that prevented use of high ASCII characters in NEXUS files (e.g. "é", "ü", and so on).
  • Fixed bug that greatly slowed file reading under Java 1.5
  • Fixed various issues to improve performance under Mac OS X Java 1.4. (Some windows are still misdrawn, but that is due to bugs in Mac OS X.)
  • Fixed other minor bugs (including, but not only: table copy/paste under Windows; use of arrow keys in matrix under Windows; retention of full character information in concatenated matrices; stepmatrix reading when character matrix ambiguous; fill tool with gaps)

Version 1.05

New Features

  • added a new Find feature (in the Edit menu) that allows you to search for sequences within DNA data matrices. The first example of a module doing this is "Matching Sequence" which finds sequences matching a target sequence the user enters. The search allows a certain number of mismatches. Optionally, it can search for the reverse, complement and reverse complement of the target sequence.
  • added a new item in the Select menu of Character Matrix Editor, "Select Lowercase Ends". This selects the ends of a DNA sequence up to the first block of N sites in a row with uppercase 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.
  • the Concatenate Matrices command will now allow molecular sequence data to be concatenated to the end of a matrix of standard categorical characters.
  • in the Mac OS X download, added an executable to run Mesquite under Java 1.4. This may be less stable than the standard version running under Java 1.3.1. The Java 1.4 version should be used only if you have Java 1.4.2 update 2 or later on Mac OS X. (The problems with early versions of Java 1.4 appear to be restricted to Mac OS X.)

Bug Fixes

  • () fixed bug in the Brownian motion simulations of continuous character evolution. Brownian motion puts more change on long branches, less change on short branches. The bug in the simulations caused this contrast between long and short branches to be heightened — long branches had even more change relative to short branches than they should have. (Inadvertantly the effect of branch length had been squared in the calculation.)

Version 1.04

New Features

  • added Utilities submenu to Tree menu of Tree Window. Currently there is only one utility, E-mail Tree, which prepares a text image of the tree and puts it in the body of an e-mail message requested using a web browser's mailto: command.

Bug fixes

  • () fixed bug in two tree simulators, Uniform speciation (Yule) and Uniform Speciation with Sampling. In versions 1.03 and before, these failed to randomize tip labels, resulting in trees whose shapes matches the model's expectations, but whose particular relationships did not. Thus, in previous versions the taxa were added one at a time to a tree growing through time. For example, if there are 6 taxa, then the divergence between the 6th taxon and its sister species was always the most recent divergence in the tree. While this would not affect questions about general tree symmetry (e.g. "What is the distribution of tree asymmetries under uniform speciation?") or branch length distributions, it would affect questions about similarity between an observed tree and those expected under a null model of speciation.
  • fixed bug that caused a crash when characters were deleted from a matrix which had annotations, images or colors attached to the cells but which didn't have footnotes.
  • fixed a few minor bugs.

Version 1.03

New Features

  • added automatic file backup, which retains copies of previously saved versions of files. This feature was added to allow the user to return to a previous version in case of errors or other problems. To enable this, in the Log window or Projects & Files window select Automatic NEXUS backup in the Defaults submenu of the File menu. Indicate the number of backups to be saved. If you enter, for instance, 3, then when you save a file named "myfile", the previous version of the file (if any) will be retained and named myfileBKP1. It will be in the same directory as myfile. The version before that will be called myfileBKP2, the version before that myfileBKP3. When you save the files again, the file ending in BKP3 will be deleted, BKP2 will be named BKP3, BKP1 renamed BKP2, and the newest backup will be called myfileBKP1.
  • enabled grayscale shading in Trace Character History for continuous-valued characters. This can be turned on in the Trace menu by selecting the "Use Grayscale If Continuous" menu item.
  • Matrices can be compared by selecting cells that differ. To request this, choose "Select by Matrix Comparison" from the Select menu of the character matrix editor. This is similar to the Utility "Compare matrices", but instead of giving a textual summary of the differences between two matrices, "Select by Matrix Comparison" highlights those cells of the matrix that differ.

Bug fixes

  • fixed a bug that caused NOTES blocks to be written in duplicate form into all linked files (opened via Link File...) if all files were saved. This bug was generally innocent except if a linked file was subsequently unlinked from the main data file. This would leave the linked file with a relictual copy of the NOTES block. If the main data file was then edited (e.g., footnotes changed, characters deleted or moved), and then the secondary file was later linked again to the main data file, its relictual (and now out of date) NOTES block could override the current NOTES block in the main file. This could cause footnotes in the main data file to revert to former ones, or to be applied to inappropriate characters or taxa. In addition to fixing this bug, we have added a warning that is given if Mesquite detects that a NOTES block is being overridden. If you suspect that your footnotes may have been corrupted by this bug, please contact us for assistance.
  • fixed a bug in Trees Directly from File (now called "Use Trees from Separate File") that gave spurious warnings.
  • fixed various other small bugs

Version 1.02

New Features

  • multiple notes with images can now be associated with taxa, characters and cells of character matrices. Prior to 1.02 a single image could be associated with each taxon, or a single footnote could be associated with each taxon, character or cell of the matrix. Now, multiple notes can be attached to each taxon, character, or cell of a matrix. Each note can have a comment, a reference, an image, and an author. Labels can be attached to the image. To use this, select the notes tool () in the Character Matrix Editor. If you touch on a cell, a Annotations window will appear with the notes for that cell, if any. Buttons in this window can be used to delete and add notes and images, and to make additional notes windows. Behavior of the window can be modified using its Annotations menu. NOTE: the single footnote system still exists and is independent of this multiple notes system.
  • MRP matrices can be generated from a set of trees, for use by Matrix Representation with Parsimony analyses to construct supertrees. To use this, select MRP Matrices from trees as a source of matrices (e.g., under Characters menu, Make New Matrix submenu).
  • a search facility has been added to the Character Matrix editor and to the List windows. The cell of the matrix found by the search is highlighted and made visible. To use this, select Find String or Find Footnote from the Edit menu. Find String searches through the row names first (e.g., taxon names for the Character Matrix Editor), then the column names (e.g., character names), then the internal cells of the table (e.g., the character state codings). Find Footnote searches the footnotes of the Character Matrix and highlights cells containing the requested text in their footnotes. You can also search for stretches of sequences or state distributions matching the currently selected stretch using Select Same Sequence and Select Same Distribution of the Select menu of the Character Matrix Editor.
  • More choices were added for coloring character matrices. Both text and background of a cell can now be colored according to properties of the cell. A paintbrush tool () was added to allow arbitrary coloring of cells of a character matrix.
  • taxa and characters can be moved by a menu item "Move Selected [taxa or characters]To..." in the List of Taxa and List of Characters windows. Prior to 1.02 taxa and characters could be moved by clicking and dragging, but using this it was difficult to move them long distances through a matrix. To use this, select the taxa or characters to be moved in their respective List window, and select Move Selected from the List menu.
  • Taxon selecting in the tree window has been modified, with a new taxon select tool ().
  • Utilities to modify taxon names have been enhanced and added to the Character Matrix Editor in the Taxon Names submenu of the Matrix menu.
  • Added import/export of FASTA files

Bug Fixes

  • () fixed calculation of Shared Partitions, which counted too many shared partitions between trees in some circumstances if the trees had different terminal taxa included
  • resolved conflict in interpetation of tree descriptions that would result in Mesquite's interpreting trees from MrBayes and other programs as having reticulations whenever labels for internal nodes were duplicated. Mesquite now interprets these labels as cosmetic only, and hence not as indicating reticulations
  • fixed bug involving the State Names Editor, by which a character might mistakenly receive a name duplicated from another character
  • fixed bug in moving taxa or characters by dragging past the end of the matrix
  • fixed bug in recoding characters by which state names and footnotes would not be adjusted
  • fixed various other small bugs

Version 1.01

New Features

  • added on-the-fly filtering and transforming of trees. Thus, trees being supplied from a file or simulation can be filtered according to various criteria or can be transformed with the available tree or branch length alterers. To use this, whenever a source of trees is needed, choose first "Filter Trees from Other Source" (if you want to select trees satisfying a criterion; more details here) or "Transform Trees from Other Source" (if you want to transform trees, e.g. reroot, scale branch lengths, etc.; more details here), then indicate what source of trees is to be filtered or transformed, and what filter or transformation is to be used.
  • added module to read trees directly from a file one at a time; allows processing of much larger tree files (>50,000 trees). To use this, request "Use Trees from Separate File" as your source of trees for charts and other calculations. You can also build a tree block from a sample of trees from a large file by selecting "Include partial contents" from the "Import File With Trees" submenu of the Taxa&Trees menu.
  • available tree and branch length alterers can be applied to all trees in a tree block. To use this, go to the Utilities submenu of the List menu of the List of Trees window.
  • added a new tree alterer: outgroup rerooting of trees. To reroot trees using a selected set of outgroups, you first must select the outgroup taxa, then, choose the menu item "Root tree with selected taxa as outgroup", for instance in the Alter/Transform Tree submenu of the Tree menu of the tree window. More details are given on the page on trees.
  • added integrated BLAST search. To use this, go to a character matrix editor window showing a molecular matrix. Select one or more stretches of sequence and choose BLAST Search from the Search submenu of the Matrix menu. Mesquite will then send a request to your web browser to perform a BLAST search at NCBI's BLAST server, one request for each of the selected stretches of sequence. The results will be available in your web browser.
  • added -w (windowless) and -b (backgroundable) flags for running long Mesquite jobs in the background in Unix from the command line
  • improved user interface of tables (List Windows, Character Matrix Editor), including navigation with arrow keys and more informative explanations and footnotes
  • Added autotab to the Character Matrix Editor. With this, the edited cell shifts automatically to the right or downward when a state is entered. To use this, select the Select and Type tool (with the letter "K") and use its drop down menu to indicate autotab right or autotab down. Autotab functions only when the Select and Type tool is the active tool.
  • selection of taxa, characters and trees is now remembered when files are saved
  • calculations of charts and Trace Character Over Trees can now be stopped part way to show partial results

Bug fixes

  • fixed tree printing bug by which node numbers and branch lengths always appeared
  • fixed bug by which pressing the Delete key while editing in a table would be misinterpreted as a requesting to delete a character, taxon or other object
  • fixed bugs in NEXUS file reading and writing (concerning SYMBOLS list, blank character names, tokenization with tab or square brackets, near-duplicate taxa blocks in same file)
  • fixed bugs in State Names Editor and Character Matrix Editor concerning footnote display and editing
  • fixed bug with Mac OS X 10.3 by which dialog boxes with lists always chose first item (this was not a bug in Mesquite, but rather in Mac OS X, but we have found a workaround)
  • fixed bug with Windows by which pie diagrams would be misdrawn as entirely black for traced characters in the Balls and Sticks tree drawing mode (this was not a bug in Mesquite, but rather in Windows/Java, but we have found a workaround)
  • several other smaller, less notable bugs were also fixed


Release Dates

2.72 11 December 2009
2.71 7 September 2009
2.7 27 August 2009
2.6 24 January 2009
2.5 9 June 2008
2.01 7 December 2007
2.0 21 September 2007
1.12 23 September 2006
1.11 21 June 2006
1.1 18 May 2006
1.06 30 August 2005
1.05 24 September 2004
1.04 1 September 2004
1.03 1 July 2004
1.02 6 May 2004
1.01 14 January 2004
1.0 22 September 2003

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