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Protocols

AWTY specifications

Information


Unique identifier OMICS_27087
Name AWTY
Alternative name are we there yet?
Interface Web user interface
Restrictions to use None
Input data Some phylogenetic trees.
Input format BEAST, BAMBE, MrBayes
Programming languages Perl
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for are we there yet?

AWTY citations

 (168)
call_split

Phylogenomics and barcoding of Panax: toward the identification of ginseng species

2018
BMC Evol Biol
PMCID: 5883351
PMID: 29614961
DOI: 10.1186/s12862-018-1160-y
call_split See protocol

[…] ysis were started using a random starting tree and were run for a total of ten million generations, sampling every 1000 generations. Four Markov runs were conducted with eight chains per run. We used AWTY to assess the convergence of the analyses []. Conflicting data within ML and Bayesian analyses were visualized and explored using the R package phangorn using the consensusNet function []. […]

call_split

Molecular Phylogeny and Dating of Forsythieae (Oleaceae) Provide Insight into the Miocene History of Eurasian Temperate Shrubs

2018
Front Plant Sci
PMCID: 5807412
PMID: 29459880
DOI: 10.3389/fpls.2018.00099
call_split See protocol

[…] to ensure that stationarity was achieved after the first 2,000,000 generations by checking whether the log-likelihood values of the sample points reached a stable equilibrium (). In addition, we used AWTY () to compare split frequencies in different runs and to plot cumulative split frequencies to ensure that stationarity was reached. The first 5000 (25%) of sampled trees from each run were discar […]

call_split

Distribution of endangered Italian gudgeon Romanogobio benacensis (Cypriniformes, Cyprinidae, Gobioninae) with remarks on distinguishing morphological characters

2018
Zookeys
PMCID: 5806454
PMID: 29430207
DOI: 10.3897/zookeys.729.20615
call_split See protocol

[…] 0 million generations and sampled every 5000 generations, with temperature parameter set to 0.2 and the first 12.5 million generations discarded as burn-in. The convergence of runs was screened using AWTY () while effective sample sizes of parameters were checked using TRACER 1.5 (). The MP analysis was performed in MEGA 6.06 (). The MP tree was obtained using the Subtree-Pruning-Regrafting algori […]

call_split

Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica

2018
PeerJ
PMCID: 5853605
PMID: 29576934
DOI: 10.7717/peerj.4337
call_split See protocol

[…] a were used to determine if the Bayesian analyses had reached convergence, and if an adequate sample of the posterior had been generated: (a) the posterior probability values tended to be stable; (b) AWTY (; ) exhibited a high correlation between the split frequencies of independent runs; (c) the average standard deviation of the split frequencies of independent runs became stable and approached z […]

library_books

Polymorphic duplicate genes and persistent non coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders

2017
BMC Genomics
PMCID: 5745709
PMID: 29281973
DOI: 10.1186/s12864-017-4358-2

[…] converged on similar results, we examined the split standard deviation for -lnL tree values among chains; values <0.01 were taken to indicate convergence. We also used the program Are We There Yet? (AWTY) [] to compare changes in the posterior probabilities of split frequencies across the independent runs.Partitioned Maximum Likelihood analyses were conducted using RAxML v.7.2.5 [] under the GTR […]

library_books

Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish

2017
PLoS One
PMCID: 5738069
PMID: 29261722
DOI: 10.1371/journal.pone.0189349

[…] ge coda [] in R environment [], and the results were close to 1.0 indicating approximate convergence. Moreover, we confirmed that the topologies of the three runs converged on the same space by using AWTY [] as implemented in the R Package RWTY []. Pseudo-ESS of the tree topologies [] was higher than 3900 for all the runs, and the average split frequencies was below 0.0002. For the time-consuming […]

Citations

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AWTY institution(s)
School of Computational Sciences, Florida State University, Tallahassee, FL, USA; Section of Evolution and Ecology, University of California, Davis, CA, USA

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