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Readme.md
repset.py

Readme.md

Protein sequence representative set selection using submodular optimization

This script selects a representative set of protein or DNA sequences from a larger set using submodular optimization. See this manuscript for more information.

Required software:

usage: repset.py [-h] --outdir OUTDIR --seqs SEQS [--mixture MIXTURE]

optional arguments:
  -h, --help         show this help message and exit
  --outdir OUTDIR    Output directory
  --seqs SEQS        Input sequences, fasta format
  --mixture MIXTURE  Mixture parameter determining the relative weight of
                         facility-location relative to sum-redundancy. Default=0.5

Output: Ordered list of sequence idenifiers, as defined in the input fasta file. The top N ids in this file represent the chosen representative set of size N.