Detecting lateral gene transfer using pairwise distances

Methods for LGT detection

parametric: GC-content, codon bias

based on phylogeney

consider only pairwise distances

detection based on discrepancy between gene and interspecies distances

probabilistic framework

detect LGTs in orthologous groups from OMA

input: group of non-paralogous sequences, at most one sequence per species

interspecies distance: mean distance in groups

result: $(f,d,r)$ where $f$ is an orthologous family, $d$ is the donor and $r$ is the receiver

statistical test of likelihood $l(f,d,r,\delta)$ against the $\chi^2$ distribution

calculation of expected distance $H_1$

comparison against GC-content, modified Clarke’s phylogenetic discordance test, perturbed distance

orthologous families are inferred using OMA’s recipe