LSx: Automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference

Carlos J. Rivera-Rivera; Juan I. Montoya-Burgos

doi:10.1101/220053

Abstract

Motivation LS³ is a recently published algorithm to reduce lineage evolutionary rate heterogeneity, a condition that can produce inference artifacts in molecular phylogenetics. The LS³ scripts are Linux-specific and the criterion to reduce lineage rate heterogeneity can be too stringent in datasets with both very long and very short branches.

Results LS^x is a multi-platform user-friendly R script that performs the LS³ algorithm, and has added features in order to make better lineage rate calculations. In addition, we developed and implemented an alternative version of the algorithm, LS⁴, which reduces lineage rate heterogeneity not only by detecting branches that are too long but also branches that are too short, resulting in less stringent data filtering.

Availability The LS^x script LSx_v.1.1.R and the user manual are available for download at: https://genev.unige.ch/research/laboratory/Juan-Montoya

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