ASTRAL
ASTRAL is a tool to estimate unrooted species trees from sets of unrooted trees. The ASTRAl algorithm uses a multi-species coalescent model and runs in polynomial time.
Topic
Phylogenetics;Molecular genetics;Statistics and probability
Detail
Operation: Phylogenetic tree generation
Software interface: Command-line user interface
Language: Java
License: Apache License 2.0
Cost: Free
Version name: 5.7.1
Credit: National Science Foundation (NSF), Howard Hughes Medical Institute (HHMI) graduate student fellowship.
Input: Newick
Output: Newick
Contact: smirarab@ucsd.edu
Collection: -
Maturity: Mature
Publications
- ASTRAL: genome-scale coalescent-based species tree estimation.
- Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, et al. (2014). ASTRAL: genome-scale coalescent-based species tree estimation. Bioinformatics 30(17): i541-8.
- https://doi.org/10.1093/bioinformatics/btu462
- PMID: 25161245
- PMC: PMC4147915
- ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes.
- Mirarab S, Warnow T. ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes. Bioinformatics. 2015 Jun 15;31(12):i44-52. doi: 10.1093/bioinformatics/btv234. PMID: 26072508; PMCID: PMC4765870.
- https://doi.org/10.1093/bioinformatics/btv234
- PMID: 26072508
- PMC: PMC4765870
- Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies.
- Sayyari E, Mirarab S (2016). Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies. Mol Biol Evol 33(7): 1654-68.
- https://doi.org/10.1093/molbev/msw079
- PMID: 27189547
- PMC: PMC4915361
- ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees.
- Zhang C, Rabiee M, Sayyari E, Mirarab S (2018). ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics 19(Suppl 6): 153.
- https://doi.org/10.1186/s12859-018-2129-y
- PMID: 29745866
- PMC: PMC5998893
- Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies.
- Sayyari E, Mirarab S (2018). Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies. Genes (Basel) 9(3).
- https://doi.org/10.3390/genes9030132
- PMID: 29495636
- PMC: PMC5867853
Download and documentation
Source: https://github.com/smirarab/ASTRAL/releases/tag/v5.7.1
Documentation: https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md
Home page: https://github.com/smirarab/ASTRAL
Links: https://github.com/smirarab/ASTRAL/blob/master/astral-tutorial.md
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