Tree-for-three-rumen-ciliates-FigShare.rar

README.txtFiles Description1) MRO-gene-trees:Phylogenetic trees of putative MRO genes of three rumen ciliates. For each gene, the homologs were obtained as described in the main text, and then tree was reconstructed by using FastTree (2.1.10) and saved in phyloxml format. The trees were named in “*.phyloxml”. On the tree, tips were annotated with an in house perl script. The trees of the three rumen ciliates were saved into three separate file folders: a) Entodinium furca-MRO, FastTree output tree in phyloxml formatb) Diplodinium dentatum-MRO, FastTree output tree in phyloxml formatc) Isotricha intestinalis-MRO, FastTree output tree in phyloxml format 2) HGT-gene-trees: Phylogeneitc trees of characterized horizontal transferred gene of three rumen ciliates. Tree was constructed by using FastTree (2.1.10)and PhyML, and saved in newick format. The trees were named in “*.nwk”.The trees of the three rumen ciliates were saved into three separate file folders, which include two subfolders(FasTree-tree and PhyML-tree):a) Efurca-HGT-NWKb) Ddentatum-HGT-NWKc) Iintestinalis-HGT-NWK

README.txt 文件说明
1) MRO基因树（MRO gene-trees）：三种瘤胃纤毛虫推定MRO基因的系统发育树。针对每个基因，同源序列按照正文所述方法获取，随后使用FastTree (2.1.10) 构建系统发育树，并以phyloxml格式保存，文件命名格式为"*.phyloxml"。使用自研Perl脚本对树的终端节点进行注释。三种瘤胃纤毛虫的系统发育树分别存储于三个独立文件夹中：
a) Entodinium furca-MRO：FastTree 输出的 phyloxml 格式系统发育树
b) Diplodinium dentatum-MRO：FastTree 输出的 phyloxml 格式系统发育树
c) Isotricha intestinalis-MRO：FastTree 输出的 phyloxml 格式系统发育树

2) HGT基因树（HGT gene-trees）：三种瘤胃纤毛虫已表征水平转移基因的系统发育树。使用FastTree (2.1.10) 与PhyML构建系统发育树，并以newick格式保存，文件命名格式为"*.nwk"。三种瘤胃纤毛虫的系统发育树分别存储于三个独立文件夹，每个文件夹包含两个子文件夹（FasTree-tree 与 PhyML-tree）：
a) Efurca-HGT-NWK
b) Ddentatum-HGT-NWK
c) Iintestinalis-HGT-NWK