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) or phylip-relaxed (names are not truncated)
    • Default: fasta
  • -c, --classes <N> The number of frequency classes in the mixture model
    • Options: 10, 20, 30, 40, 50, or 60
    • Default: 60
  • -o, --output <out_dir> Path to user-defined output directory
    • Default: ./mammal_modeler_out_<M.D.Y>
  • -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 the esmodel.nex file
    • 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.