CITATION.cff

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cff-version: 1.2.0
title: PHYling for Phylogenomic reconstruction from genomes
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Jason
    family-names: Stajich
    name-particle: E
    email: jason.stajich@ucr.edu
    affiliation: University of California-Riverside
    orcid: 'https://orcid.org/0000-0002-7591-0020'
  - given-names: Cheng-Hung
    family-names: Tsai
    email: chenghung.tsai@email.ucr.edu
    affiliation: University of California-Riverside
    orcid: 'https://orcid.org/0000-0003-3419-2146'
repository-code: 'https://github.com/stajichlab/PHYling'
url: 'https://lab.stajich.org/projects/'
abstract: >-
  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.
keywords:
  - phylogenomics
license: MIT
version: '2.0'
date-released: '2023-04-27'