AGAP, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France.
Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554, CNRS, EPHE, IRD, Université de Montpellier, Montpellier, France.
Mol Biol Evol. 2018 Oct 1;35(10):2582-2584. doi: 10.1093/molbev/msy159.
Multiple sequence alignment is a prerequisite for many evolutionary analyses. Multiple Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program that explicitly accounts for the underlying codon structure of protein-coding nucleotide sequences. Its unique characteristic allows building reliable codon alignments even in the presence of frameshifts. This facilitates downstream analyses such as selection pressure estimation based on the ratio of nonsynonymous to synonymous substitutions. Here, we present MACSE v2, a major update with an improved version of the initial algorithm enriched with a complete toolkit to handle multiple alignments of protein-coding sequences. A graphical interface now provides user-friendly access to the different subprograms.
多序列比对是许多进化分析的前提。多编码序列比对程序（MACSE）是一个多序列比对程序，它明确考虑了蛋白质编码核苷酸序列的潜在密码子结构。其独特的特点允许即使在存在移码的情况下，也能构建可靠的密码子比对。这有助于下游分析，例如基于非同义替换与同义替换的比值来估计选择压力。在这里，我们介绍 MACSE v2，这是一个重大更新，初始算法的改进版本以及用于处理蛋白质编码序列的完整工具包。现在，图形界面为不同子程序提供了用户友好的访问。
