A simple utility I set up to gather ad-hoc scripts written in Bash or Perl to do stuff I do often like computing GC-contents for a bacterial species, downloading sequence from genbank, converting Clustal output from MUSCLE to Fasta and computing the position of divergence in a multi-fasta file.

biotk bacterial-gc-content <species-name>
biotk clustal-to-fasta < <STDIN>
biotk fasta-snp-pos <multi-fasta-file.fasta> <reference-name>
biotk genbank-query [options] <query>

Detailed description of each subcommand can be found with :

$ biotk <subcommand> --help

Computes the mean GC content of prokaryotic species as reported in genomes reports on NCBI.

Converts an alignment in CLW format to a multi-fasta one.

Computes the position of divergence in a multi-fasta alignment.

Query and download Genbank for a given accession number.

Samuel Barreto

[email protected] twitter : @samuel_barreto8

GNU Public Licence 3 (detailed in the COPYING file.)