FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

作者：Patrick Kück, Gary C. Longo · 发表于：Frontiers in Zoology · 年份：2014 · DOI：10.1186/s12983-014-0081-x · 被引用次数：689 · 研究领域：Genomics and Phylogenetic Studies、Genome Rearrangement Algorithms、Evolution and Paleontology Studies

BACKGROUND: Phylogenetic and population genetic studies often deal with multiple sequence alignments that require manipulation or processing steps such as sequence concatenation, sequence renaming, sequence translation or consensus sequence generation. In recent years phylogenetic data sets have expanded from single genes to genome wide markers comprising hundreds to thousands of loci. Processing of these large phylogenomic data sets is impracticable without using automated process pipelines. Currently no stand-alone or pipeline compatible program exists that offers a broad range of manipulation and processing steps for multiple sequence alignments in a single process run. RESULTS: Here we present FASconCAT-G, a system independent editor, which offers various processing options for multiple sequence alignments. The software provides a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation between nucleotide and amino acid states, consensus generation of specific sequence blocks, sequence concatenation, model selection of amino acid replacement with ProtTest, two types of RY coding as well as site exclusions and extraction of parsimony informative sites. Convieniently, most options can be invoked in combination and performed during a single process run. Additionally, FASco...