Multiple sequence alignment
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Updated: Aug 8, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Robert C Edgar1, Serafim Batzoglou
1bob@drive5.com
Abstract:
Multiple sequence alignments are an essential tool for protein structure and function prediction, phylogeny inference and other common tasks in sequence analysis. Recently developed systems have advanced the state of the art with respect to accuracy, ability to scale to thousands of proteins and flexibility in comparing proteins that do not share the same domain architecture. New multiple alignment benchmark databases include PREFAB, SABMARK, OXBENCH and IRMBASE. Although CLUSTALW is still the most popular alignment tool to date, recent methods offer significantly better alignment quality and, in some cases, reduced computational cost.
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