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