PairWise Alignment
Local tools available on sura (our unix server)
- EMBOSS programs:
needle - global alignment
water - local alignment - FASTA programs:
align - global alignment
lalign - local alignment - BLASTpackage program bl2seqs
Web tools
- BL2seq at NCBI
- LALIGN- Local alignment of 2 sequences (Pearson) at Viriginia university or at EMBNET, CH
- Dialign2 or at Bielfeld
- Align - global alignment (using Lipman and Pearson algorithm)
Multiple Alignment
Local tools
-
EMBOSS programs - available on sura (unix server) or on sura web
edialign - Local multiple alignment
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
dialign2 - aligns 2 or more sequences, based on segment-to-segment comparison
t_coffee - a multiple sequence alignment package
muscle - multiple alignment software
Web tools
- open in new windowClustal Omega at EBI - Alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments
- BLOCKS Maker - WWW server for multiple alignments
- open in new windowKalign Very fast MSA tool that concentrates on local regions. Suitable for large alignments
- open in new windowMAFFT Multiple Alignment using Fast Fourier Transform
- open in new windowUCSC HMM Application
- open in new windowSAM Sequence Alignment and Modeling System
- open in new windowthe MEME suite multiple EM for motif elicitation
- open in new windowWebLogo creating Sequences logo at Berkeley
- open in new windowDIALIGN - finding local similarities among distantly related sequences
- open in new windowT_COFFE suite A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
- open in new windowMuscle MUltiple Sequence Comparison by Log- Expectation, at EBI
open in new windowMusclei download
Multiple Alignment Editors
Web tools
- open in new windowBOXSHADE - Pretty Printing and Shading of Multiple-Alignment filesi
- open in new windowAMAS - Analyse Multiply Aligned Sequences