ASTRAL statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ASTRAL

Tool usage distribution map

This map represents all the scientific publications referring to ASTRAL per scientific context
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Associated diseases

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ASTRAL specifications


Unique identifier OMICS_06055
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




No version available



  • person_outline Tandy Warnow

Publications for Accurate Species TRee ALgorithm

ASTRAL citations


Multiple origins of green blood in New Guinea lizards

Sci Adv
PMCID: 5955620
PMID: 29774232
DOI: 10.1126/sciadv.aao5017

[…] d no support for Prasinohaema monophyly among more than 4000 individually estimated gene trees (tables S2 and S3) (). In addition, modeling for incomplete lineage sorting using a coalescent approach (ASTRAL) yielded topologies that were concordant with our unpartitioned ML approach (RAxML), indicating that our data were robust to problems of incomplete lineage sorting. Despite strong support for f […]


Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

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

[…] th 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) substitu […]


Practical considerations for plant phylogenomics

Appl Plant Sci
PMCID: 5895195
PMID: 29732268
DOI: 10.1002/aps3.1038

[…] ments (e.g., see Johnson et al., ).Sequence alignments generated by target capture can be concatenated into a supermatrix or used for gene‐tree‐based methods of phylogenetic reconstruction, including ASTRAL‐III (Mirarab et al., ; Zhang et al., ), ASTRID (Vachaspati and Warnow, ), and BUCKy (Larget et al., ). This is especially useful with exon capture and Hyb‐Seq approaches, because loci are likel […]


Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics

Appl Plant Sci
PMCID: 5895186
PMID: 29732266
DOI: 10.1002/aps3.1036

[…] For phylogeny estimation, we used a concatenation‐, partition‐based approach using maximum likelihood (CA‐ML) and two methods, ASTRAL (Mirarab and Warnow, ) and singular value decomposition quartets (SVDquartets; Chifman and Kubatko, ), that are statistically consistent under a coalescent process. To reconstruct the CA‐ML tre […]


Comparison of taxon‐specific versus general locus sets for targeted sequence capture in plant phylogenomics

Appl Plant Sci
PMCID: 5895190
PMID: 29732262
DOI: 10.1002/aps3.1032

[…] with 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 data i […]


Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

PMCID: 5867853
PMID: 29495636
DOI: 10.3390/genes9030132

[…] ene trees was to reduce the gene tree estimation error. Alternatively, one can simply remove branches with support at or below a certain threshold in gene trees and use the resulting tree as input to ASTRAL []. With this procedure and the support threshold set to 10%, we generated a new ASTRAL tree based on all 14,446 unbinned gene trees from the avian dataset [,] (b). The resulting tree was large […]

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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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