ASTRAL protocols

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ASTRAL specifications

Information


Unique identifier OMICS_06055
Name ASTRAL
Alternative name Accurate Species TRee ALgorithm
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Input data Some trees.
Input format NEWICK
Output data A file providing the species tree topology, branch lengths in coalescent units, branch supports measured as local posterior probabilities and possible annotations with other quantities.
Output format NEWICK
Operating system Unix/Linux
Programming languages Java, Shell (Bash)
Computer skills Advanced
Version 5.6.1
Stability Stable
Maintained Yes

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  • person_outline Tandy Warnow <>

Publications for Accurate Species TRee ALgorithm

ASTRAL in pipeline

2016
PMCID: 5144963
PMID: 27672114
DOI: 10.1534/g3.116.034744

[…] for each subset, the concatenation phylogeny and the coalescent-based phylogeny, as well as their clade support values (bootstrap support and ic values), were separately estimated using ra×ml and astral by following the procedures described above., all data matrices and their resulting phylogenies have been deposited on the figshare repository at doi: 10.6084/m9.figshare.3370675., contig […]


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ASTRAL in publications

 (63)
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] sorted to ensure that each resampled data set was resampled by loci and by sites (). the 100 resampled data sets were used to infer species trees in a summary coalescent framework, implemented in astral-ii 4.7.8 () that allows unrooted, multifurcating trees as input and has been shown to be robust to effects of both incorrectly estimated gene trees and gene tree heterogeneity (). extended […]

PMCID: 5937819
PMID: 29690866
DOI: 10.1186/s12864-018-4683-0

[…] 100 bootstrap replicates [] under protgammaijttf model as recommended by prottest.3.4.2 []. phylogenetic reconstruction was performed with all gene sets using the coalescence method implemented in astral v5.5.6 []. the genetic distance between two species was calculated based on the sequence alignment concatenated from the 160 alignments using phylip [] with jones-taylor-thornton (jtt) […]

PMCID: 5895190
PMID: 29732262
DOI: 10.1002/aps3.1032

[…] their greater average length and high proportion of variable sites, are also suited to the inference of well‐supported gene trees, which are necessary for a number of species tree methods (e.g., accurate species tree algorithm [astral]; mirarab and warnow, )., designing a general target locus set for a group does not require multiple genomic resources, but some source of genomic sequence […]

PMCID: 5867853
PMID: 29495636
DOI: 10.3390/genes9030132

[…] and biological datasets, we show that the null hypothesis is rejected for all but the shortest branches, and in most cases, it is retained for true polytomies. the test, available as part of the accurate species tree algorithm (astral) package, can help systematists decide whether their datasets are sufficient to resolve specific relationships of interest., phylogenies are typically modeled […]

PMCID: 5829825
PMID: 29487238
DOI: 10.1128/mBio.01219-17

[…] oryzae pathotype triticum clade 2. orange dots, representatives of pyricularia oryzae pathotype oryza. download fig s1, pdf file, 0.5 mb., next, we used the multilocus data as input to the program astral with the goal of inferring a species tree that takes into account possible discrepancies among individual gene genealogies (). the astral tree failed to provide strong support for the branch […]


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ASTRAL institution(s)
Department of Electrical and Computer Engineering, University of California at San Diego, Gilman Drive, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, CA, USA
ASTRAL funding source(s)
Supported by the National Science Foundation grant IIS-1565862 and the NSF grant ACI-1053575.

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