GET_HOMOLOGUES: a versatile software package for pan-genome analysis
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README.md

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

This software is maintained by Bruno Contreras-Moreira (bcontreras at eead.csic.es) and Pablo Vinuesa (vinuesa at ccg.unam.mx). The original version, suitable for bacterial genomes, was described in:

Contreras-Moreira B, Vinuesa P (2013) Appl. Environ. Microbiol. 79:7696-7701

Vinuesa P, Contreras-Moreira B (2015) Methods in Molecular Biology Volume 1231, 203-232

The software was then adapted to the study of intra-specific eukaryotic pan-genomes resulting in script GET_HOMOLOGUES-EST, described in:

Contreras-Moreira B, Cantalapiedra CP et al (2017) Front. Plant Sci. 10.3389/fpls.2017.00184

GET_HOMOLOGUES-EST has been tested with genomes and transcriptomes of Arabidopsis thaliana and Hordeum vulgare, available at http://floresta.eead.csic.es/plant-pan-genomes. It was also used to produce the Brachypodium distachyon pangenome at https://brachypan.jgi.doe.gov.

A tutorial is available, covering typical examples of both GET_HOMOLOGUES and GET_HOMOLOGUES-EST.

A Docker image is available with GET_HOMOLOGUES bundled with GET_PHYLOMARKERS, ready to use. The GET_PHYLOMARKERS manual explains how to use clusters from with GET_HOMOLOGUES to compute robust multi-gene and pangenome phylogenies.

The code is regularly patched (see CHANGES.txt in each release and TODO.txt), and has been used in a variety of studies (see citing papers here and here, respectively).

We kindly ask you to report errors or bugs in the program to the authors and to acknowledge the use of the program in scientific publications.

Funding: Fundacion ARAID, Consejo Superior de Investigaciones Cientificas, DGAPA-PAPIIT UNAM, CONACyT, FEDER, MINECO, DGA-Obra Social La Caixa.

logo CSIC logo ARAID logo UNAM

Installation instructions are summarized on README.txt and full documentation is available in two flavours:

version HTML
original, for the analysis of bacterial pan-genomes manual
EST, for the analysis of intra-species eukaryotic pan-genomes, tested on plants manual-est