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AnGST specifications

Information


Unique identifier OMICS_23377
Name AnGST
Alternative name ANalyzer of Gene and Species Trees
Interface Web user interface
Restrictions to use None
Input data A specie tree or gene tree.
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Eric Alm
  • person_outline ANGST team

Publication for ANalyzer of Gene and Species Trees

AnGST citations

 (14)
library_books

Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces

2017
MBio
PMCID: 5472806
PMID: 28588130
DOI: 10.1128/mBio.00644-17

[…] sing RAxML for each gene family, and FastTree was used to generate a phylogeny for each bootstrapped alignment. These 10 bootstrap trees were then used as the gene tree inputs for each gene family in AnGST. Reconciliation event costs used were selected based on the criteria suggested in the original AnGST publication (). Their weights for LGT and gene loss events were selected to minimize the mean […]

library_books

Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant Associated Habitats

2016
Front Microbiol
PMCID: 5169363
PMID: 28066362
DOI: 10.3389/fmicb.2016.02039

[…] A parsimony-based reconciliation approach, AnGST, was used to understand the history of the PA genomic evolution events (David and Alm, ). The reconciliation was obtained by inferring a minimum set of evolutionary events between the gene- and […]

library_books

Adaptive radiation by waves of gene transfer leads to fine scale resource partitioning in marine microbes

2016
Nat Commun
PMCID: 5036157
PMID: 27653556
DOI: 10.1038/ncomms12860

[…] The Aly and Oal gene trees were reconciled against the reference phylogeny using AnGST with the following cost parameters: loss=1.0, duplication=2.0, HGT=3.0 (ref. ). The optimal reconciliation was the reconciliation with the lowest total event score. We also modified the AnGST so […]

library_books

Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

2016
Front Microbiol
PMCID: 4921485
PMID: 27446038
DOI: 10.3389/fmicb.2016.00998

[…] ains of the marine-derived subgroup can assimilate phosphate under phosphate-limiting conditions, and only four strains in the other subgroup have the effective pathway. Furthermore, according to the AnGST results, the gene-tree species-tree reconciliation allows us to infer the evolutionary history of every gene family in an explicit fashion. For the example of TRAP-T, there are four clusters of […]

library_books

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression

2016
PLoS Biol
PMCID: 4898821
PMID: 27276034
DOI: 10.1371/journal.pbio.1002475

[…] The AnGST algorithm [] was used to infer horizontal gene transfer, gene duplication, and gene loss of CAZy domains across the Streptomyces phylogeny. The protein sequences for dbCAN annotated domain famil […]

library_books

Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity

2015
BMC Genomics
PMCID: 4396162
PMID: 25888333
DOI: 10.1186/s12864-015-1474-8

[…] ee supported by 1000 bootstrap replicates was computed with FastTree []. Gain, loss, and HGT events were inferred by reconciliation of the gene trees and the species complex tree topologies using the AnGST algorithm (Analyzer of Gene and Species Tree) []. This algorithm compares the topology of a gene tree with its associated species tree, which is generally defined as an explicit phylogenetic met […]

Citations

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AnGST institution(s)
Computational & Systems Biology Initiative, Massachusetts Institute of Technology, Cambridge, MA, USA; Departments of Biological Engineering & Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; The Broad Institute, Cambridge, MA, USA
AnGST funding source(s)
Supported by the US Department of Energy ENIGMA project through contract DE-AC02-05CH11231, the National Science Foundation under an Assembling the Tree of Life Award, and a National Defense Science and Engineering Graduate Fellowship.

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