Longest gene search tool

Summary

Tool for finding list of gene-like sequences of max common length for given input list of sequences (aligned contigs). Input is in FASTA format, output is in FASTA-2 format.

Requirements

• Python 3.6+
• BioPython 1.71+

Parameters

• -i, --input-file: input FASTA file with aligned contigs.
• -o, --output-file: path to output FASTA-2 file.
• -ms, --min-similarity: Minimal allowed similarity of sequences, in [0, 1] interval. By default is 0.95.

Example

python3 ./longest_gene.py -i examples/gregalis.fa -o output.fa