Alignment of Biological Sequences with Jalview
James B Procter, G. Mungo Carstairs, Ben Soares, Kira Mourão, T. Charles Ofoegbu, Daniel L. Barton, Lauren Michelle Lui, Anne Menard, Natasha Sherstnev, David Roldan-Martinez, Suzanne Duce, David Martin, Geoffrey J. Barton
Abstract
In this chapter, we introduce core functionality of the Jalview interactive platform for the creation, analysis, and publication of multiple sequence alignments. A workflow is described based on Jalview's core functions: from data import to figure generation, including import of alignment reliability scores from T-Coffee and use of Jalview from the command line. The accompanying notes provide background information on the underlying methods and discuss additional options for working with Jalview to perform multiple sequence alignment, functional site analysis, and publication of alignments on the web.