Authors Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2.

Galaxy integration Julie Baffard and ABiMS TEAM, Roscoff Marine Station

Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.

Credits : Gildas le Corguillé, Misharl Monsoor

Description

This tool searches for different homologous genes from pairwise comparisons between a set of fasta files (one file per species).

Parameters

• 'Input files' : a collection of fasta files (one file per species)
• 'e_value' : the blast e-value. By default it's 1e-5.
• 'Alignment tool' : choose the sequences alignment tool between tblastx and Diamond. tblastx is more sensitive and Diamond is much faster.

Outputs

• 'Pairwise' : the general output. It gives the information about what the tool has done for each pairwise.
• 'Pairwise_DNA' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are in nucleic format. There are one file per couple of species, and homologous pairs are written by sets of 4 lines :

Exemple for two homologous pairs for the output file for species X/Y :

The AdaptSearch Pipeline