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PHYling website  

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.

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.

The marker sets developed for this approach in fungi are available as part of the 1KFG Phylogenomics_HMMs project resource.

Environment Modules

Run module spider PHYling to find out what environment modules are available for this application.

System Variables

  • HPC_PHYLING_DIR - installation directory
  • HPC_PHYLING_BIN - executable directory


If you publish research that uses PHYling you have to cite it as follows:

Stajich JE. 2017 PHYling: Phylogenomic pipeline from core markers on genomes to unassembled reads.