LS: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference.

  • publication
  • 15-08-2019

Rivera-Rivera CJ, Montoya-Burgos JI. BMC Bioinformatics 2019 Aug;20(1):420. 10.1186/s12859-019-3020-1. 10.1186/s12859-019-3020-1. PMC6693147.

Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS, a data subselection algorithm that, by removing fast-evolving sequences in a gene-specific manner, identifies subsets of sequences that evolve at a relatively homogeneous rate. However, this algorithm had two major shortcomings: (i) it was automated and published as a set of bash scripts, and hence was Linux-specific, and not user friendly, and (ii) it could result in very stringent sequence subselection when extremely slow-evolving sequences were present.

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