Phyml

From Vd

Contents 1 General description 2 Application homepage 3 Proper citation 4 Input file formats 5 Output files

General description

PHYML is a software implementing a new method for building phylogenies from DNA and protein sequences using maximum likelihood. Data sets can be analyzed under several models of evolution (JC69, K80, F81, F84, HKY85, TN93 and GTR for nucleotides and Dayhoff, JTT, mtREV, WAG, DCMut, RtREV, CpREV, VT, Blosum62 and MtMam for amino acids). A discrete-gamma model (Yang, 1994) is implemented to accommodate rate variation among sites. Invariable sites can also be taken into account.

Source code is available upon request, see application homepage.

Application homepage

PHYML - A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood

Proper citation

St�phane Guindon and Olivier Gascuel, "A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood", Syst. Biol, 52(5):696-704, 2003.

Input file formats

The input sequence file is a standard PHYLIP file of aligned DNA or amino-acids sequences. See application home page for details.

Output files

• <sequence file name>_phyml_lk.txt : likelihood value(s)
• <sequence file name>_phyml_tree.txt : inferred tree(s)
• <sequence file name>_phyml_stat.txt : detailed execution stats
• <sequence file name>_phyml_boot_trees.txt : bootstrap trees (special case)
• <sequence file name>_phyml_boot_stats.txt : bootstrap statistics (special case)