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

ABSTRACT:

Background

Lineage rate heterogeneity can be a major source of bias, especially in multi-gene phylogeny inference. We had previously tackled this issue by developing LS³, 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.

Results

We address these challenges and produce a new, platform-independent program, LS^X, written in R, which includes a reprogramm

SUBMITTER: Rivera-Rivera CJ 

PROVIDER: S-EPMC6693147 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature