p3-count-families

Count Protein Families in Genomes

p3-count-families.pl [options]

This script will count the number of occurrences of each protein family found in the specified genomes. The output will contain the family ID, the associated product, the number of total occurrences, and the number of genomes containing the family.

Parameters

There are no positional parameters.

The standard input can be overridden using the options in Input Options, and is used to specify the genomes of interest. The column containing the genome ID can be specified using the options in Column Options. The following additional command-line options are supported.

• singly

If specified, only single-occurrence families will be counted.

• type

The type of protein family– local, global, or figfam. The default is global.

• verbose

Write status messages to STDERR.