Documentation¶

`mfpcluster`¶

mfpcluster clusters the sequences of a fasta file over a range of similarity values using CD-HIT.

Inputs
- -i, –in [input_fasta]
  
  The fasta file to cluster.
Outputs
- A directory containing:
  0.n.fa.clstr: The clusters found by CD-HIT when clustering input_fasta at similarity threhsold n.
  
  0.n.fa: Fasta files containing the representative sequences for the clusters found when clustering input_fasta at similarity threshold n.
  
  <input_fasta>.log: A plain-text document containing diagnostic information from the current run of mfpcluster.
  
  command.cluster.sh: A newline separated document containing the commands passed to CD-HIT to perform clustering.
  
  cluster_counts.tsv: A tsv containing with columns for the similarity threshold clustered at, the number of clusters found at that simlarity threshold, and the first-order difference calculated at that point.
Optional arguments
- -o, –out [string] (Default: <input_fasta>.clustering)
  
  The name of the output directory.