STELLS

STELLS is a tool to infer species trees from gene tree topologies. The STELLS algorithm uses coalescent-based maximum likelihood and includes functions for inference with haplotypes and to compute the Gene Tree Probability with the Multispecies Coalescent.

Topic

Phylogenetics;Statistics and probability;Evolutionary biology;Genetics

Detail

  • Operation: Phylogenetic tree analysis

  • Software interface: Command-line user interface

  • Language: C++

  • License: GNU General Public License v3.0

  • Cost: Free

  • Version name: 2.2.0.1

  • Credit: National Science Foundation (NSF), National Institutes of Health (NIH).

  • Input: -

  • Output: -

  • Contact: Yufeng Wu yufeng.wu@uconn.edu

  • Collection: --

  • Maturity: Mature

Publications

  • A coalescent-based method for population tree inference with haplotypes.
  • Wu Y. A coalescent-based method for population tree inference with haplotypes. Bioinformatics. 2015 Mar 1;31(5):691-8. doi: 10.1093/bioinformatics/btu710. Epub 2014 Oct 24. PMID: 25344500; PMCID: PMC4341064.
  • https://doi.org/10.1093/bioinformatics/btu710
  • PMID: 25344500
  • PMC: PMC4341064
  • An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree.
  • Wu Y (2016). An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree. Bioinformatics 32(12): i225-i233.
  • https://doi.org/10.1093/bioinformatics/btw261
  • PMID: 27307621
  • PMC: PMC4908345
  • STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies.
  • Pei J, Wu Y (2017). STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies. Bioinformatics 33(12): 1789-1797.
  • https://doi.org/10.1093/bioinformatics/btx079
  • PMID: 28186220
  • PMC: -

Download and documentation

< Back to DB search