3. Relative rates sister-clades analysis

This folder contains the input and output files used in and obtained from the program Phyltest (Phyltest v.2.0, http://www.kumarlab.net/publications) for the sister-clade relative rates analysis. This folder is organised into subfolders by source study name and then by gene. The numbers at the beginning of the folder names do not have significance and are only used for organisational purposes. Transitions are identified by the set# in the file name (e.g. “Set1” or “S1” = transition #1, transitions as described in the Supplementary Material). All transitions were analysed with separate input and output files except for the transitions within the source study folder Cunha et al. 2011 where each transition was run from the same file per gene. Within the input files the abbreviations FL=flightless, F=flight-capable, OG=outgroup, and the number after these identifiers signifies the transition. Each gene folder (except where just described) contains 2 files per transition: 1 input file (nucleotide - “.dat”) and 1 output file.本文件夹包含用于姐妹支（sister-clade）相对速率分析、且由Phyltest软件（Phyltest v.2.0，http://www.kumarlab.net/publications）生成与使用的输入与输出文件。 本文件夹按照来源研究名称进行分组，再依据基因进一步划分为子文件夹。 文件夹名称开头的数字无实际意义，仅用于组织管理。 转换（transitions）由文件名中的set编号标识，例如"Set1"或"S1"代表转换#1，相关转换规则详见补充材料。 除来源研究文件夹Cunha等（2011）中的转换外，所有转换均采用独立的输入与输出文件进行分析；该文件夹下每个基因的所有转换均共享同一输入文件。 输入文件中使用的缩写如下：FL=无飞行能力（flightless）、F=有飞行能力（flight-capable）、OG=外类群（outgroup），这些标识后的数字代表对应转换的编号。 除前文所述特殊情况外，每个基因子文件夹中每个转换对应2个文件：1个核苷酸序列输入文件（后缀为".dat"）与1个输出文件。