category: Molecular Markers
programs:

atv  Draw and edit phylogenetic trees

blmarker  bioLegato interface for discrete state data (eg. molecular markers)

csv2phyl.sh  >>> csv2phyl.sh is obsolete. Instead, use phylcnv.py which handles a larger number of file formats

dollop  Discrete data parsimony method of DOLLO

drawgram  Draw cladograms

drawtree  Draw radial trees

fitch  Distance trees  Fitch/ Margoliash

genographer  Score markers from gel images

kitsch  Distance trees  Fitch/ Margoliash (molecular clock)

Mapmaker  Create genetic maps using marker and phenotype data

MapmakerQTL  Create maps for QTL data

mGDE  GDE interface for discrete state data (eg. molecular markers)

mix  Mixed method discrete character parsimony

neighbor  Distance trees  NeighborJoining/UPGMA

phylcnv.py  Convert Phylip files to and from other formats

restdist  Compute distance matrices for discrete data

restml  Maximum likelihood phylogeny for discrete data

treedist  Calculate distance between trees

treetool  Phylogenetic tree editor

v_concat  Concatenates a set of sequence alignments.

v_demograph  Estimates demographic parameters (effective population size, growth rate) by maximizing the coalescent prior for a single given clocklike tree.

v_disttree  Tree methods dealing with distance matrices.

v_evolve  Generates artificial data sets for a tree and a model of sequence evolution (available models are the same as in MLTREE and MLDIST)

v_mldist  Computes pairwise maximumlikelihood distance matrices for nucleotide, amino acid, and twostate data under a variety of substitution models

v_mltree  Computes likelihoods of trees under a variety of substitution models (see MLDIST)

v_reroot  Reads a treefile (NH format) and reroots the tree, making node the new root.

v_rewrite  Reads a data set and reformats it into various formats

v_showtree  Reads treefile (NH format), generates ASCII picture, and computes distance matrix induced by branch length.

v_splitcodon  Separate 1st, 2nd, 3rd codon positions of an alignment into separate file.

v_treecomp  Reads two trees, each from a different file, and computes the Robinson Foulds score (topological distance measure based on splits).