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A script in R to run the LS³ and LS⁴ phylogenetic data subsampling algorithms for reducing lineage rate heterogeneity
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LSX is a script in R that runs the LS³ and LS⁴ algorithms of data subsampling for multigene phylogenetic inference. Both of these algorithms do a gene-by-gene inspection of the heterogeneity of evolutionary rates among user-defined lineages of interest (LOI). Then, using criteria that differ in both algorithms (see details here or in the papers), they try to find a subsample of sequences that evolve at a homogeneous rate across all LOIs. If this subset is found, an alignment of the gene is produced with only the sequences that evolve homogeneously. At the same time, a table is also produced showing which sequences were “flagged” (the sequences that were removed), and which sequences were kept. If a subset of sequences that evolve at a homogeneous rate is not found, the gene is flagged entirely.


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