| description | fastDNAml is a program for estimating maximum likelihood phylogenetic trees from nucleotide sequences. |
| version | 1.2.2 |
| homepage | http://iubio.bio.indiana.edu/soft/molbio/evolve/fastdnaml/fastDNAml.html |
| commands | fastDNAml fastDNAml_boot fastDNAml_loop clean_checkpoints frequencies transition jumble global quickadd outgroup usertree userlengths treefile printdata categories weights fastdnaml |
| manpages | fastDNAml |
| documentation | |
| interfaces | fastdnaml |
| description | Computer Program Package for Molecular Phylogenetics. |
| version | 2.3b2 |
| homepage | http://www.ism.ac.jp/ismlib/softother.e.html#molphy |
| commands | protml protst nucml nucst njdist totalml |
| manpages | |
| documentation | |
| interfaces |
| description | a BASH script to improve ML tree search with PhyML 3.* |
| version | 1.14 |
| homepage | |
| commands | morePhyML |
| manpages | |
| documentation | |
| interfaces | morephyml |
| description | A Python Package for Phylogenetics |
| version | 0.87.r132 |
| homepage | http://www.nhm.ac.uk/research-curation/research/projects/p4/index.html |
| commands | p4 |
| manpages | |
| documentation | |
| interfaces |
| description | PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. |
| version | 4.4c |
| homepage | http://abacus.gene.ucl.ac.uk/software/paml.html |
| commands | baseml codeml basemlg mcmctree pamp evolver yn00 chi2 |
| manpages | |
| documentation | |
| interfaces |
| description | PHYML - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. |
| version | 3.0.1 |
| homepage | http://code.google.com/p/phyml |
| commands | phyml |
| manpages | |
| documentation | |
| interfaces | phyml |
| description | A program built to compute phylogenetic trees in cases where events of homologous recombination have affected an alignment. Based on original phyml (c) Stephane Guindon |
| version | 2.4.4 |
| homepage | http://pbil.univ-lyon1.fr/software/phyml_multi/ |
| commands | phyml_multi PartitioningHMM.py PartitioningMM.py |
| manpages | |
| documentation | |
| interfaces |
| description | TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. |
| version | 5.2 |
| homepage | http://www.tree-puzzle.de/ |
| commands | puzzle |
| manpages | |
| documentation | |
| interfaces | puzzle |
| description | Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. |
| version | 1.3.2 |
| homepage | http://tree.bio.ed.ac.uk/software/seqgen/ |
| commands | seq-gen |
| manpages | |
| documentation |
http://bioweb2.pasteur.fr/docs/seq-gen/ |
| interfaces | seqgen |