mammal_modeler.py
Generate a MAMMaL site heterogeneous model for a user defined number of classes.
mammal_modeler.py [OPTIONS] -m <input_matrix>
Required arguments:
-tr
,--tree <input.tre>
Path to tree in Newick format-m
,--matrix <matrix.fas|nex|phy>
Path to supermatrix
Optional arguments:
-if
,--in_format <format>
Input format of matrix- Options:
fasta
,nexus
,phylip
(names truncated at 10 characters) orphylip-relaxed
(names are not truncated) - Default:
fasta
- Options:
-c
,--classes <N>
The number of frequency classes in the mixture model- Options:
10
,20
,30
,40
,50
, or60
- Default:
60
- Options:
-o
,--output <out_dir>
Path to user-defined output directory- Default:
./mammal_modeler_out_<M.D.Y>
- Default:
-h
,--help
Show this help message and exit
Default mammal_modeler.py
output:
- a directory
mammal_modeler_out_<M.D.Y>
that contains:- a file
esmodel.nex
- nexus file that contains the MAMMaL mixture model. This file can be used to fit a mixture model in IQtree using the options-m LG+ESmodel+G -mdef esmodel.nex
- NOTE: Do not use
+F
(i.e., LG+ESmodel+G+F) when using this model. Instead use (LG+ESmodel+G). The overall amino acid frequencies are already presented in theesmodel.nex
file
- NOTE: Do not use
- a file
estimated_frequencies
- a tab-delimited output file that each row gives the amino acid frequencies for a class. This file is output by MAMMaL, but is not used further here. See the MAMMaL documentation for more information.
- a file