Mercurial > repos > padge > astral
diff test-data/README @ 0:66ebc4b19d6c draft default tip
"planemo upload for repository https://github.com/smirarab/ASTRAL commit 0f93f327c49e93d6af057973d68ba772ba5715dc-dirty"
author | padge |
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date | Wed, 13 Apr 2022 15:03:31 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/README Wed Apr 13 15:03:31 2022 +0000 @@ -0,0 +1,17 @@ +**Song et al**: +We include here sample input files based on the [Song et al.](http://www.pnas.org/content/109/37/14942.short) dataset of 37 mammalian species and 442 genes. +We have removed 23 problematic genes (21 mislabeled genes and 2 genes we classified as outliers) and +we have also re-estimated gene trees using RAxML on the alignments that authors of that paper kindly provided to us. +We have also included 200 replicates of bootstrapped gene trees for the gene trees we estimated on the Song et al. dataset. + +**Simulation**: +We have included simulations based on the Song et al. dataset with increases rates of ILS. + +**primates:** +We have also created a reduced version of the Song et al. dataset with 9 primates, tree shrews, and 4 other mammalian taxa. This dataset is provided for testing the exact version. + +**14 taxon simulation:** +Simulated used SimPhy with extreme levels of ILS + +**100-taxon simulations:** +A simulated dataset with 100 taxa and 2500 bootstrap replicate gene trees is also provided for testing large datasets.