Data from: AMAS: a fast tool for large alignment manipulation and computing of summary statistics

The amount of data used in phylogenetics has grown explosively in the recent years and many phylogenies are inferred with hundreds or even thousands of loci and many taxa. These modern phylogenomic studies often entail separate analyses of each of the loci in addition to multiple analyses of subsets of genes or concatenated sequences. Computationally efficient tools for handling and computing properties of thousands of single-locus or large concatenated alignments are needed. Here I present AMAS (Alignment Manipulation And Summary), a tool that can be used either as a stand-alone command-line utility or as a Python package. AMAS works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. The manipulation functions include conversions among popular formats, concatenation, extracting sites and splitting according to a pre-defined partitioning scheme, creation of replicate data sets, and removal of taxa. The statistics calculated include the number of taxa, alignment length, total count of matrix cells, overall number of undetermined characters, percent of missing data, AT and GC contents (for DNA alignments), count and proportion of variable sites, count and proportion of parsimony informative sites, and counts of all characters relevant for a nucleotide or amino acid alphabet. AMAS is particularly suitable for very large alignments with hundreds of taxa and thousands of loci. It is computationally efficient, utilizes parallel processing, and performs better at concatenation than other popular tools. AMAS is a Python 3 program that relies solely on Python’s core modules and needs no additional dependencies. AMAS source code and manual can be downloaded from http://github.com/marekborowiec/AMAS/ under GNU General Public License.近年来，系统发育学（phylogenetics）领域所使用的数据量呈爆发式增长，诸多系统发育树的推断基于数百乃至数千个基因座（loci）与大量分类群（taxa）。这些现代系统基因组学研究往往需要对每个基因座开展单独分析，同时还要针对基因子集或串联序列进行多次分析。当前亟需可高效处理数千个单基因座或大型串联序列联配（alignment）并计算其相关属性的计算工具。本文介绍AMAS（联配操作与汇总工具，Alignment Manipulation And Summary），该工具既可以作为独立的命令行实用程序（command-line utility）运行，也可作为Python包（Python package）使用。AMAS支持氨基酸与核苷酸序列联配，兼具序列操作功能与基础统计量计算能力。其序列操作功能涵盖主流格式间的转换、序列串联、位点提取、基于预定义分区方案的联配拆分、重复数据集生成以及分类群移除等。所计算的统计量包括分类群数量、联配长度、矩阵单元格总数、未确定字符总数量、缺失数据占比、（针对DNA联配的）AT与GC含量、变异位点的数量与占比、简约信息位点的数量与占比，以及与核苷酸或氨基酸字母表相关的全部字符计数。AMAS尤其适配包含数百个分类群与数千个基因座的超大型联配数据集，其计算效率优异，支持并行处理，且在序列串联操作上的表现优于其他主流工具。AMAS是一款基于Python 3开发的程序，仅依赖Python核心模块，无需额外依赖项。AMAS的源代码与使用手册可从http://github.com/marekborowiec/AMAS/ 下载，采用GNU通用公共许可证（GNU General Public License）授权。