GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas

Frontiers in Microbiology
Pablo VinuesaBruno Contreras-Moreira

Abstract

The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phyloge...Continue Reading

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Citations

May 30, 2019·International Journal of Systematic and Evolutionary Microbiology·Philippe M de LajudiePeter Young
May 8, 2019·Molecular Biology and Evolution·Mario A Cerón-RomeroL A Katz
Jan 27, 2020·Current Microbiology·Julissa Enciso-IbarraBruno Gomez-Gil
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Aug 28, 2020·Frontiers in Microbiology·Rajender KumarAnders Sjöstedt
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Dec 7, 2021·International Journal of Systematic and Evolutionary Microbiology·Renato PedronOlivier Jousson

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Software Mentioned

BWA
omega
CLUSTAL
BDBH
_ HOMOLOGUES
FT
hcluster
GET
COGtriangles
amphora

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