fast_site_remover.py

Remove the fastest evolving sites within a phylogenomic supermatrix in a stepwise fashion.

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

Required arguments:

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

Optional arguments:

• -s, --step_size <N> Size of removal step (i.e., 3000 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: ./fast_site_removal_out_<M.D.Y> with sub-directories:
    • steps_N
• -h, --help Show this help message and exit

fast_site_remover.py output:

• a directory called ./fast_site_removal_out_<M.D.Y> with:
  • sub-directories steps_<N> (N=step size) that contain:
    • alignment files of the input matrix with N fastest sites removed iteratively until exhaustion
  • a file DE.dat&&
  • a file rate&&
  • dist_est.ctl&&

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