heterotachy.py

Remove the most heterotachious sites from a phylogenomic supermatrix in a stepwise fashion.

heterotachy.py -tr <input_tree> -m <input_matrix> [OPTIONS]

Required arguments:

  • -tr, --tree <input.tre> Path to tree in Newick format
  • -m, --matrix <matrix.fas|nex|phy> Path to supermatrix

Optional arguments:

  • -s, --step_size <N> Size of removal step (i.e., 1000 sites removed) to exhaustion.
    • Default: 3000
  • -f, --out_format <format> Desired format of the output matrices.
    • Options: fasta, nexus, phylip (names truncated at 10 characters) or phylip-relaxed (names are not truncated)
    • Default: fasta
  • -o, --output <out_dir> Path to user-defined output directory.
    • Default: ./heterotachy_out_<M.D.Y>
  • -h, --help Show this help message and exit.

Default heterotachy.py output

  • a directory heterotachy_out_<M.D.Y> that contains:
    • slow.tre - tree file in Newick format containing a tree pruned from the input tree and contains only taxa determined to be slow-evolving.
    • fast.tre - tree file in Newick format containing a tree pruned from the input tree and contains only taxa determined to be fast-evolving.
    • slow.phy - phylip formatted file containing only slow-evolving taxa.
    • fast.phy - phylip formatted file containing only fast-evolving taxa.
    • slow.dist_est.ctl - control file to be used by dist_est for slow-evolving taxa.
    • fast.dist_est.ctl - control file to be used by dist_est for fast-evolving taxa.
    • slow.DE.dat&& - an output of the dist_est operation on slow.phy and slow.tre.
    • slow.rate_est.dat&& - an output of the dist_est operation on slow.phy and slow.tre.
    • fast.DE.dat&& - an output of the dist_est operation on fast.phy and fast.tre.
    • fast.rate_est.dat&& - an output of the dist_est operation on fast.phy and fast.tre.
    • a subdirectory steps_<N> (N=step size) that contains the files:
      • step<0-N>.phy - phylip formatted matrix files with N less sites than the previous step to exhaustion.

&& These are standard dist_est input/output files. See the dist_est documentation for a more detailed explanation of their contents.