Principe - Needleman & Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed. From these findings it is possible to determine whether significant homology exists between the proteins. This information is used to trace their possible evolutionary development. The maximum match is a number dependent upon the similarity of the sequences. One of its definitions is the largest number of amino acids of one protein that can be matched with those of a second protein allowing for all possible interruptions in either of the sequences. Comparisons are made from the smallest unit of significance, a pair of amino acids, one from each protein.
SeaView. Version 4.7 NEW: bootstrap support optionally with the "Transfer Bootstrap Expectation" method NEW: trimming-rule to shorten long sequence names in phylogenetic trees NEW: 64-bit version for the MS Windows platform NEW: multiple-tree windows NEW: seaview uses PHYLIP v3.696 to compute parsimony trees NEW: seaview can be run without GUI using a command line NEW: seaview drives the PhyML v3.1 program to compute maximum likelihood phylogenetic trees. NEW: seaview drives the Gblocks program to select blocks of conserved sites. NEW: seaview drives the Clustal Ω v1.2 program to perform multiple sequence alignment. SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.
Screen shots of the main alignment and tree windows. Dialog window to perform Maximum-Likelihood tree-building. Reference. MAFFT - a multiple sequence alignment program. Clustal (Omega) "The last alignment program you'll ever need" Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. Please note that Clustal Omega is currently a command line-only tool. A full description of the algorithms used by Clustal Omega is available in the Molecular Systems Biology paper Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Clustal Omega can be run online at the following websites (this list will expand in the coming months).
Please that webservers may have limitations on maximum alignment size not present in the standalone version. Help Citing Clustal View ChangeLog News: MUSCLE.