DNA and Protein Pairwise and Multiple Alignment

Pairwise Alignment
Multiple Alignment
Multiple Alignment Editors

PairWise Alignment

Local tools

EMBOSS programs - available on sura
needle - global alignment
water - local alignment

FASTA programs - available on sura
align - global alignment
lalign - local alignment

BLAST programs - available on sura
bl2seq - local alignment

Remote tools

open in new windowBL2seq at NCBI
open in new windowSIM - Finds a user-defined number of best non-intersecting alignments between two protein sequences, at Expasy server
LALIGN- Local alignment of 2 sequences (Pearson) at open in new windowViriginia university or at EMBNET, CH
open in new windowDialign at Pastuer, or at Bielfeld
open in new windowSearch for Proteins at PIR
open in new windowGeneWise at EBI, compares a protein sequence to a genomic DNA sequence

Multiple Alignment

Local tools

EMBOSS programs - available on sura
emma - Multiple alignment program - interface to ClustalW program
infoalign - Information on a multiple sequence alignment
plotcon - Plots the quality of conservation of a sequence alignment
prettyplot - Displays aligned sequences, with colouring and boxing
showalign - Displays a multiple sequence alignment
tranalign - Align nucleic coding regions given the aligned proteins

Command line programs on sura
clustalW - multiple sequence alignment program
muscle - Multiple Protein sequences comparison by log-expectatio
t_coffee - multiple sequence alignment
dialign2 - aligns 2 or more sequences, based on segment-to-segment comparison

Remote tools

open in new windowClustalW - Alignment of multiple sequences using the ClustalW algorithm at PBI, or ClustalW at EBI
open in new windowMUSCLE - Multiple PROTEIN sequences comparison by log-expectation at EBI
open in new windowT_COFFEE - multiple sequence alignment at EBI, and T-Coffee at Notredame's Lab
open in new windowCobalt at NCBI, computes a multiple protein sequence alignment using conserved domain and local sequence similarity information
open in new windowProbCons - Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences at Max-Plant institute
open in new windowwebPRANK alignment algorithm at EBI
open in new windowKalign - A fast and accurate multiple sequence alignment algorithm at SBC
open in new windowMEME - multiple EM for motif elicitation
open in new windowBLOCKS Maker - WWW server for multiple alignments
open in new windowUCSC HMM Application - method for iterative SAM HMM construction and remote homology detection
open in new windowSAM Sequence Alignment and Modeling System
open in new windowMatchBox - protein sequence multiple alignment tools based on strict statistical criteria in Belgium
open in new windowDIALIGN - finding local similarities among distantly related sequences
open in new windowLAMA Block vs Bl ock Searcher at Fred Hutchinson Cancer Research Center
open in new windowMultAlin - Multiple sequence alignment with hierarchical clustering by Florence Corpet
open in new windowMAFFT - Multiple Sequence Alignment based on fast Fourier transform
open in new windowRevTrans takes a set of DNA sequences, virtually translates them, and aligns the peptide sequences
open in new windowGblocks Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Multiple Alignment Editors

Remote tools

open in new windowWebLOgo - Sequence logos at Berkley
open in new windowBioconductor SeqLogo- Sequence logos
open in new windowBOXSHADE - Pretty Printing and Shading of Multiple-Alignment files
open in new windowAMAS - Analyse Multiply Aligned Sequences
open in new windowSeq2Logo Protein sequence logo method
open in new windowSeqLogos Sequence logo from amino acid alignment
open in new windowPLOGO Protein Sequence Logos using Relative Entropy