Pangenomic Analysis of theRhizobialesUsing the GET_HOMOLOGUES Software Package

Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids

“…These features demonstrate the flexibility and robustness of the software, and highlight its ease of use. There are several other interesting features, such as the analysis of syntenic intergenic regions, the use of the synteny criterion to define orthologs, the use of the BerkeleyDB system to trade speed for RAM when analyzing very large genomic datasets, which are well documented in the manual and have been published elsewhere [5,27]. Altogether these features make GET_HOMOLOGUES a useful, versatile, flexible and powerful piece of software that allows non-specialists to make rigorous and detailed analyses of microbial pan-genomics and comparative genomics.…”

“…We are now set to proceed with the actual calculations. We have recently shown that the definition of orthologous clusters and their composition are variable depending on the clustering method used [5,27]. Technical details aside, it is clear that the most robust orthologous gene clusters would be those recognized by all three clustering algorithms currently implemented in GET_HOMOLOGUES.…”

“…Figure 1b (see Note 7). The pan-genome matrix is also provided in PHYLIP format, which can then be used by parse (bundled with the GET_HOMOLOGUES package) from the PHYLIP package [30] to compute pan-genomic parsimony trees, as we have shown previously [5,27] and detail in the GET_HOMOLOGUES manual. Using the -T flag will do this automatically.…”