A snakemake workflow for phylogenomic analysis of genome clusters.
kizuchi is a snakemake
workflow for building gene trees, starting from a collection of genomes
and HMM profiles, and then analyzing the phylogenetic histories of alleles
within genome-level ANI clusters. The aim of this workflow is to automate and
document gene tree analysis in a reproducible way, with the ultimate objective
of tracing recombination across timescale domains.
- gene prediction using
prodigal-gv - gene annotation using
hmmer - ortholog scoring
- amino acid alignment using
clustalo - alignment trimming using
trimal - tree inference using
fasttree - genome clustring using
fastANI - phylogenetic correlations using
SuchTree
