Multiple alignments

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Jalview Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. JalviewLite is the web based version of Jalview, and used on many web sites (there's a list of some here)The Jalview Desktop is for biologists and bioinformaticians who need to create, curate, analyse and publish multiple sequence alignments. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. Jalview
Download Jalview Get the latest Jalview Desktop application: Alternately, download an installer for your system from the InstallAnywhere Jalview Installers page.InstallAnywhere is a Java program installation system. It will work out which operating system you have, and present you with the package it considers most appropriate. You can download the Jalview application installation on its own, and optionally download a copy of the Java Virtual Machine which actually runs Jalview. Problems ? Take a look at the FAQs. Download Jalview
MUSCLE There are two papers. The first (NAR) introduced the algorithm, and is the primary citation if you use the program. The second (BMC Bioinformatics) gives more technical details, including descriptions of non-default options. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32(5):1792-1797 [Link to PubMed]. Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113 [Link to PubMed]. MUSCLE