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:
The software was then adapted to the study of intra-specific eukaryotic pan-genomes resulting in script GET_HOMOLOGUES-EST, described in:
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.
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:
|original, for the analysis of bacterial pan-genomes||manual|
|EST, for the analysis of intra-species eukaryotic pan-genomes, tested on plants||manual-est|