Tool stats & trends
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|Alternative name||are we there yet?|
|Interface||Web user interface|
|Restrictions to use||None|
|Input data||Some phylogenetic trees.|
|Input format||BEAST, BAMBE, MrBayes|
Publication for are we there yet?
Phylogenomics and barcoding of Panax: toward the identification of ginseng species
[…] 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 . […]
Molecular Phylogeny and Dating of Forsythieae (Oleaceae) Provide Insight into the Miocene History of Eurasian Temperate Shrubs
[…] 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 […]
Distribution of endangered Italian gudgeon Romanogobio benacensis (Cypriniformes, Cyprinidae, Gobioninae) with remarks on distinguishing morphological characters
[…] 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 […]
Out of Asia: mitochondrial evolutionary history of the globally introduced supralittoral isopod Ligia exotica
[…] 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 […]
Polymorphic duplicate genes and persistent non coding sequences reveal heterogeneous patterns of mitochondrial DNA loss in salamanders
[…] 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 […]
Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish
[…] 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 […]
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