DOI: 10.6084/m9.figshare.7874612.v1
title: Datasets and Software from Wang and Liu BMC Genomics 2016

description: Datasets and software used in paper "A performance study of the impact of recombination on species tree analysis"<br>=================================================================================================================<br>The dataset and software are provided in a compressed file.The compressed file has been split into multiple pieces to facilitate file hosting.To reassemble and decompress the compressed file, run the following commands (assuming that thefiles are stored on a Linux computer):<br> cd local_directory_where_the_compressed_file_pieces_are_located cat wang-and-liu-2016-data.tar.gz.split-* &gt; wang-and-liu-2016-data.tar.gz tar xzf wang-and-liu-2016-data.tar.gz<br>=================================================================================================================<br>Dataset and software files are arranged in the following directory structure. All the trees are in Newick format.<br>1. ./simulated-model-trees: - it contains 8-taxon, 15-taxon, and 25-taxon simulated model trees. <br>2. ./alternate-model-trees: - it contains the species trees(species_trees.nex) used in Lanier and Knowles' study and the empirical tree (empirical_tree.nex) used in our study.<br>3. ./empirical-SNPs: - chr#.meta: it is the meta file for chromosome#, which maps the loci of the SNPs to its actual positions in the full sequence alignment. - chr#.fasta: FASTA format SNPS of chromosome# - map: map the taxa in chr#.fasta to the species.<br>4. ./software: - ms: used to simulate coalescent trees. [Download][ms_link] - msHOT: used to simulate coalescent trees with recombination hotspots. [Download][mshot_link] - Seq-gen: used to simulate DNA sequence alignment along the coalescent trees.[Download][seq-gen_link] - ASTRAL: used to infer model species tree from coalescent trees.[Download][astral_link] - FastTree: used to infer tree from DNA sequence alignment.[Download][fasttree_link] - LRScan_con.py: implementation of LRScan algorithm.<br>5. The sequence data is contained in the following subdirectories: - ./sequence_data/EP: contains the sequence data simulated from empirical tree. - ./sequence_data/LN: contains the sequence data simulated from species trees used in Lanier and Knowles' study. - ./sequence_data/HOT: contains the sequence data simulated from 8-taxa model trees under deterministic approach (hot1) and non-deterministic approach (hot2). - ./sequence_data/three-case: contains the sequence data simulated from 8-taxa, 15-taxa, 25-taxa model trees. - Within each subdirectory, the folders "100", "200", "1000" indicates the recombination rate of during the sequence generation process.<br>=================================================================================================================<br>[ms_link]:http://home.uchicago.edu/rhudson1/source/mksamples.html[mshot_link]:http://home.uchicago.edu/~rhudson1/source/mksamples.html[seq-gen_link]:http://tree.bio.ed.ac.uk/software/seqgen/[astral_link]:https://github.com/smirarab/ASTRAL[fasttree_link]:http://www.microbesonline.org/fasttree/[seq_link]:https://www.dropbox.com/s/e48j2bcnyxdg2yi/sequence_data.tar.gz?dl=0<br>=================================================================================================================<br>You can redistribute the data and software and/or modifyit under the terms of the GNU General Public License as published bythe Free Software Foundation, either version 3 of the License, or(at your option) any later version.<br>This data and software is distributed in the hope that it will be useful,but WITHOUT ANY WARRANTY; without even the implied warranty ofMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See theGNU General Public License for more details.<br>You should have received a copy of the GNU General Public Licensealong with this program. If not, see .<br>