Data set: Australia's hidden radiation - phylogenomic analysis reveals rapid Miocene radiation of blindsnakes

This repository contains the additional raw data to accompany our paper entitled "Australia’s hidden radiation: phylogenomic analysis reveals rapid Miocene radiation of blind snakes."

This project is part of the AusARG Initiative funded by BioPlatforms Australia.

Raw sequences data can be downloaded from the BioPlatforms downloads portal: https://data.bioplatforms.com/dataset?q=ticket%3ABPAOPS-1196

Information about files

1. ASTRAL_tree_SqCL_AHE.tre - output from ASTRAL-III just with SqCL data + outgroups
2. ASTRAL_tree_SqCL_AHE_Ramphotyphlops.tre - same with above but also  including additional Ramphotyphlops genes.
3. mcmctree_1.txt - mcmcfile output from MCMCTree analysis using all SkewT or SkewNormal distribution priors.
4. mcmctree_2.txt - mcmcfile output from MCMCTree analysis using SkewT, SkewNormal, and cauchy distribution priors. **This is the tree used in our publication**
5. mcmctree_strategy1.tre - output phylogeny 1
6. mcmctree_strategy2.tre - output phylogeny 2
7. IQTREE_gcf_scf.nex - gene concordance and site factors for mcmctree_strategy2.tre

tree_data/ folder contains concatenated gene trees (IQTREE) and corresponding shortcut coalescent method (ASTRAL-III) tree.

Should there be questions regarding the code and data set, please contact the corresponding author.