RASER
RASER is a likelihood based method for testing and detecting site-specific evolutionary rate shifts.
Given a multiple sequence alignment (MSA) and a phylogenetic tree, the program determines:
(a) Whether or not site-specific rate shifts characterize the evolution of a protein, and
(b) If so, points to the specific sites and lineages in which these shifts have most likely occurred.
Software & Data
SELECTON
Selecton is a web-server for the detection of site-specific evolutionnary rates, measured as Ka/Ks, the ratio between the non-synonymous to synonymous rate at each site.
LGT3STATE
LGT3State - detecting lateral gene transfer via swapping of two non-homologous enzymes
PARALLEL SELECTION
ParaSel - detecting parallel selection in phylogenetic data: sites where two or more substitutions occurred in independent lineages of the phylogeny, and were driven by selection.
INFERRING POP-GEN PARAMS FROM TIME-SERIES
FITS - Inferring population genetics parameters (fitness, mutation rate, or population size) from temporal deep sequencing data.