This repository contains all scripts used in our paper, A Comparative Study of SVDquartets and Other Coalescent-Based Species Tree Estimation Methods.
##Simulated Datasets The original, unprocessed simulated datsets used in this study were obtained from the following:
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The 11-taxon datasets M1, M2, M3, and M4 with varying levels of ILS was obtained from http://www.cs.utexas.edu/~bayzid/files/10-taxon.tar.bz
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The 15-taxon dataset with a pectinate model species tree was obtained from http://www.cs.utexas.edu/users/phylo/datasets/weighted-binning-datasets.html under the "15-taxon datasets" link.
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The 37-taxon mammalian simulated dataset with AD=18% was obtained from https://www.ideals.illinois.edu/handle/2142/55319 under the link "Sequence Alignments and Trees for Mammalian 2X for Mirarab et. al."
##Linux Executables for Species Tree Estimation Methods The linux executables for ASTRAL [1], NJst [2], FastTree [3], and RAxML [4] are in the phylogenetic_tools folder. The linux executable for PAUP* [5] is in the src-pipelines folder.
##Scripts for Running Species Tree Estimation Methods on the Simulated Datasets
The files in each "pipeline-" folder are a combination of shell scripts and qsub scripts for the UIUC campus cluster.