Data from the article "The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models"

Data from the article:

"The mitochondrial phylogeny of land plants shows support for Setaphyta under non-stationary substitution models"

Filipe de Sousa, Peter Civáň, João Brazão, Peter G. Foster, Cymon J. Cox

These data are divided in four folders:

* 1_36_gene_nt_alignments_&_trees - contains 36 single gene nucleotide alignments and the corresponding trees inferred from a MCMC analysis on the program p4

* 2_36_gene_aa_alignments_&_trees - contains 36 single gene amino acid alignments and the corresponding trees inferred from a MCMC analysis on the program p4

* 3_concatenated_alignments_&_trees - contains the nucleotide, codon-degenerate and amino acid alignments of 36 concatenated genes and the corresponding trees inferred from MCMC analyses on the programs p4 and phylobayes with composition homogeneous, tree-heterogeneous and site-heterogeneous models; trees correspond to figures S1-S7 on the online supplemental file.

* 4_concatenated_ML_trees - contains the ML trees from the analyses of the concatenated datasets (nucleotide, codon degenerate and amino acid).

本文数据集来源于以下研究论文：

《陆生植物线粒体系统发育：非平稳替换模型下支持Setaphyta类群》

作者：Filipe de Sousa、Peter Civáň、João Brazão、Peter G. Foster、Cymon J. Cox

本数据集分为四个文件夹：

* 1_36_gene_nt_alignments_&_trees：包含36个单基因核苷酸序列比对文件，以及通过p4软件开展马尔可夫链蒙特卡洛（MCMC）分析所得到的对应系统发育树
* 2_36_gene_aa_alignments_&_trees：包含36个单基因氨基酸序列比对文件，以及通过p4软件开展MCMC分析所得到的对应系统发育树
* 3_concatenated_alignments_&_trees：包含36个串联基因的核苷酸、密码子简并及氨基酸序列比对文件，以及通过p4与phylobayes软件，基于组分均一模型、树异质性模型及位点异质性模型开展MCMC分析所得到的对应系统发育树；该部分树文件对应在线补充材料中的图S1至S7
* 4_concatenated_ML_trees：包含基于串联数据集（核苷酸、密码子简并及氨基酸数据集）分析得到的最大似然（Maximum Likelihood, ML）系统发育树