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 was benchmarked with genomes and transcriptomes of Arabidopsis thaliana and Hordeum vulgare, available at http://floresta.eead.csic.es/plant-pan-genomes, and used to analyze the pan-genomes of Brachypodium distachyon and Brachypodium hybridum (press release).
A tutorial is available, covering typical examples of both GET_HOMOLOGUES (bacteria) and GET_HOMOLOGUES-EST (plants).
A Docker image is available with GET_HOMOLOGUES bundled with GET_PHYLOMARKERS, ready to use. The GET_PHYLOMARKERS manual explains how to use nucleotide & peptide clusters produced by GET_HOMOLOGUES to compute robust multi-gene and pangenome phylogenies.
The code is regularly patched (see CHANGES.txt in each release, 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.
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 |