rtc_binner.py

Bin orthologs based on relative tree certainty score and construct supermatrices from the bins.

rtc_binner.py [OPTIONS] -i <input_dir>

Required arguments:

  • -i, --input <input_dir> Path to directory containing single gene trees built from only orthologs, corresponding bootstrap value files, and corresponding alignments.

Optional arguments:

  • --in_format <format> Format of the input files
    • Options: fasta, nexus, phylip (names truncated at 10 characters), or phylip-relaxed (names are not truncated)
    • Default: fasta
  • --out_format <format> Desired format of the output files
    • 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: ./rtc_binner_out_<M.D.Y>
  • -p, --prefix <prefix> Prefix of input files
    • Default: NONE
    • Example: path/to/input/prefix*
  • -s, --suffix <suffix> Suffix of input files
    • Default: NONE
    • Example: path/to/input/*suffix
  • -h, --help Show this help message and exit

rtc_binner.py output:

  • a directory ./rtc_binner_out_<M.D.Y> with 7 subdirectories:
    • matrix_constructor25/ that contains:
      • supermatrix (matrix, stats, and indices) of the top 25% RTC scored orthologs
    • matrix_constructor50/ that contains:
      • supermatrix (matrix, stats, and indices) of the top 50% RTC scored orthologs
    • matrix_constructor75/ that contains:
      • supermatrix (matrix, stats, and indices) of the top 75% RTC scored orthologs
    • rtc25/ that contains:
      • alignments of the top 25% RTC scored orthologs
    • rtc50/ that contains:
      • alignments of the top 50% RTC scored orthologs
    • rtc75/ that contains:
      • alignments of the top 75% RTC scored orthologs