PHYling for Phylogenomic reconstruction from genomes

The unified PHYling pipeline for phylogenomic data collection from annotated genomes. This is latest iteration of tool for using phylogenetically conserved markers to pull out informative gene or protein info from genomic and transcriptomic datasets in order to construct gene trees and species phylogenies. The aligned markers can be extracted from protein sequences for phylogenetic analyses and also projected into coding sequence alignments for codon-based analyses for better resolution of recently diverged species. This approach can also utilize BUSCO generated marker sets to obtain markers from unannotated genomes. The assumptions in this approach are that the markers are generally single copy in genomes and taking best hit is sufficient first approximation for identifying orthologs.