Bioinformatics & Genomics
Multiple Alignment & Phylogeny
Editors & Formatters
Servers & Software for Generating Alignments
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BCM Search Launcher: Pairwise Sequence Alignment
[Baylor College of Medicine] A site with multiple tools to align pairs of input sequences.
Computational Services at EMBL
[EMBL] Ties together sequence search and retrieval, alignment, data submission, comparison and prediction into one site. Also available are tools for structure verification and related software.
[Laboratories of Molecular Biophysics, Rockefeller University] ModView is a plugin to visualize and analyze multiple biomolecule structures and/or sequence alignments. It is also used as a database interface in several structure-sequence protein resources: ModBase (database of Comparative Protein Structure Models), LigBase (Structural Database of Aligned Ligand Binding Protein Sequences), and DBAli (database of sequence-structure alignments. ModView can be also used to view structures and sequences in Protein Data Bank.
Multiple Alignment Resource Page
[VSNS BioComputing Division - University of Bielefeld] A calculation of Multiple Alignment resources on the World Wide Web.
[EMBL] Permits the user to submit a sequence for prediction. Links to other pages for multiple sequence alignment, prediction of secondary structure, prediction of solvent accessibility, prediction of transmembrane helices, prediction of topology for transmembrane proteins, fold recognition by prediction-based threading, and evaluation of secondary structure prediction accuracy.
Programs for biosequence analysis
This page contains example implementations in Java of some algorithms for pairwise alignment (including the Needleman-Wunsch algorithm), hidden Markov models (HMMs), and phylogenetic trees. Some are available as Java applets you can run from this page.
[MRC Laboratory of Molecular Biology] A Perl5 program that evaluates the accuracy of protein sequence alignments with very low sequence identity.
Tools for Multiple Alignments
[Pôle Bio-Informatique Lyonnais] A list of pointers to information sources useful for multiple alignment of homologous sequences.
TOP and MAPS
[Lund University] Pairwise/multiple alignment and similarity searches in databases for three dimensinal protein structures.