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

Motivation LS 3 is a recently published algorithm to reduce lineage evolutionary rate heterogeneity, a condition that can produce inference artifacts in molecular phylogenetics. The LS 3 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 LS 3 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, LS 4 , 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