GB-to-TNT: facilitating creation of matrices from GenBank and diagnosis of results in TNT

GOLOBOFF, PABLO A.; CATALANO, SANTIAGO

Riverside, CA

Congreso; XXXI International Meeting of the Willi Hennig Society; 2012

Willi Hennig Society

This paper presents a pipeline, implemented in an open-source programcalled GB-to-TNT (GenBank-to-TNT), for creating large molecular matrices,starting from GenBank files and finishing with TNT matrices whichincorporate taxonomic information in the terminal names. GB-to-TNT isdesigned to retrieve a defined genomic region from a bulk of sequencesincluded in a GenBank file. The user defines the genomic region to beretrieved and several filters (genome, length of the sequence, taxonomicgroup, etc.); each genomic region represents a different data block in thefinal TNT matrix. GB-to-TNT first generates Fasta files from the inputGenBank files, then creates an alignment for each of those (by calling analignment program), and finally merges all the aligned files into a single TNTmatrix. The new version of TNT can make use of the taxonomic informationcontained in the terminal names, allowing to easily diagnose results, evaluatethe fit between the trees and the taxonomy, and automatically label or colortree branches with the taxonomic groups they represent.