modelmatcher 1.0

Rapid identification of sequence evolution models

modelmatcher: Rapid identification of evolutionary models

This tool reads multiple sequence alignments and determines a suitable sequence evolution model for your phylogenetic analysis.

Usage

Example usage:

$ modelmatcher inputfile.fasta

Options

Input formats

Input format is detected automatically from the following list, but can also be requested specifically.

• FASTA
• Phylip
• Nexus
• Clustal
• Stockholm

Output

Output is given as a simple text table, or in JSON format for easy parsing by other scripts, ranking possible models in preference order. For example, the command above may yield a table looking like:

WAG             7.972
VT              8.238
BLOSUM62        8.478
JTT             8.864
JTT-DCMUT       8.917
LG              9.984
DCMUT          10.467
Dayhoff        10.495
FLU            11.211
HIVb           12.853
RtREV          14.048
cpREV          14.186
HIVw           17.338
MtZoa          18.476
MtMAM          21.453
mtArt          21.741
MtREV          22.059

Each model is given with its modelmatcher score.

Alternatively, the same analysis can look like:

$ modelmatcher  --json  inputfile.fasta
{"n_observations": 863692, "infile": "inputfile.fasta", "n_seqs": 66, "model_ranking": [["WAG", 7.972410383355675], ["VT", 8.238362164888876], ["BLOSUM62", 8.478000205922985], ["JTT", 8.863578165338444], ["JTT-DCMUT", 8.917496451351846], ["LG", 9.983874357603963], ["DCMUT", 10.466872509785343], ["Dayhoff", 10.49522598111376], ["FLU", 11.21137482805874], ["HIVb", 12.852877789672046], ["RtREV", 14.047539707772572], ["cpREV", 14.18648653904322], ["HIVw", 17.338193829402], ["MtZoa", 18.475515151949153], ["MtMAM", 21.452528293860837], ["mtArt", 21.740741039472418], ["MtREV", 22.058622800684176]]}

Install

Recommended installation is:

pip install --upgrade pip
pip install alv