rid

rid: sequence file reformatting and identifier normalization

Purpose

To reformat multiple sequence files, including multiple sequence alignments, and to replace long names with shorter identifiers.

If used in phylogenetic analysis, the original, long, names can be added to phylogenetic trees using decorator.

Download

• • Most current version (might be unstable): forester.jar

• Source code is available at GitHub: https://github.com/cmzmasek/forester

Usage

% java -Xmx1024m -cp path/to/forester.jar org.forester.application.rid [options] <input sequences file> [output sequences file name] [output map file name]

Options

• -o=<format>: output format: "fasta" or "f" for Fasta (default), "phylip" or "p" for Phylip, "nexus" or "n" for Nexus

• -s: to replace sequence names with short(er) identifiers

Example

% rid -s -o=p my_seqs.fasta

last updated: 2017-09-06