Datasets and Software from Wang and Liu BMC Genomics 2016

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>

论文"重组对物种树分析影响的性能研究"所用数据集与软件
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本研究所用数据集与软件均打包于压缩文件中。为便于文件托管，该压缩文件已拆分为多个分卷。若需合并并解压该压缩文件，请在Linux系统中执行以下命令（假设分卷文件已存储于目标目录）：
cd 存储压缩文件分卷的本地目录
cat wang-and-liu-2016-data.tar.gz.split-* > wang-and-liu-2016-data.tar.gz
tar xzf wang-and-liu-2016-data.tar.gz
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数据集与软件文件的目录结构如下，所有进化树文件均采用Newick格式（Newick format）：
1. ./simulated-model-trees：包含8分类群、15分类群及25分类群的模拟模型树。
2. ./alternate-model-trees：包含Lanier与Knowles研究中所用的物种树文件species_trees.nex，以及本研究所用的经验树文件empirical_tree.nex。
3. ./empirical-SNPs：
- chr#.meta：染色体#的元数据文件，用于将SNP位点映射至全序列比对的实际位置。
- chr#.fasta：染色体#的FASTA格式（FASTA format）SNP序列文件。
- map：将chr#.fasta中的分类群名称映射至对应物种。
4. ./software：
- ms：用于模拟溯祖树（coalescent trees），[下载地址][ms_link]
- msHOT：用于模拟带有重组热点的溯祖树，[下载地址][mshot_link]
- Seq-gen：用于沿溯祖树模拟DNA序列比对，[下载地址][seq-gen_link]
- ASTRAL：用于从溯祖树推断模型物种树，[下载地址][astral_link]
- FastTree：用于从DNA序列比对推断进化树，[下载地址][fasttree_link]
- LRScan_con.py：LRScan算法的Python实现代码。
5. 序列数据存储于以下子目录：
- ./sequence_data/EP：包含基于经验树模拟得到的序列数据。
- ./sequence_data/LN：包含基于Lanier与Knowles研究中所用物种树模拟得到的序列数据。
- ./sequence_data/HOT：包含基于8分类群模型树，分别通过确定性方法（hot1）与非确定性方法（hot2）模拟得到的序列数据。
- ./sequence_data/three-case：包含基于8分类群、15分类群及25分类群模型树模拟得到的序列数据。
- 每个子目录下的100、200、1000文件夹分别代表序列生成过程中的重组率参数。
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[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
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本数据集与软件可根据自由软件基金会发布的GNU通用公共许可证（第3版或任意后续版本）的条款进行再分发及/或修改。
本数据集与软件的发布仅出于实用目的，不附带任何明示或默示的担保，包括但不限于适销性或特定用途适用性的担保。有关详细信息，请参阅GNU通用公共许可证。
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