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