LSCF Bioinformatics - Target/Protein

PairWise Alignment

EMBOSS programs - available on dapsas/inn or from the WEB
needle - global alignment
water - local alignment

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

Command line programs
dialign - aligns 2 or more sequences, based on segment-to-segment comparison

open in new windowSIM - Finds a user-defined number of best non-intersecting alignments between two protein sequences, at Expasy server
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)
SSearch at PIR

EMBOSS programs - available on dapsas/inn or from the WEB
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
clustalW - multiple sequence alignment program
clustalX - X-windows interface for clustalW
muscle - Multiple Protein sequences comparison by log-expectatio
t_coffee - multiple sequence alignment
probcons - Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
dialign2 - aligns 2 or more sequences, based on segment-to-segment comparison
seaview - X-windows multiple sequence alignment editor

Clustal 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
Kalign Very fast MSA tool that concentrates on local regions. Suitable for large alignments
MAFFT Multiple Alignment using Fast Fourier Transform
UCSC HMM Application
SAM Sequence Alignment and Modeling System
the MEME suite multiple EM for motif elicitation
WebLogo creating Sequences logo at Berkeley
DIALIGN - finding local similarities among distantly related sequences
T_COFFE suite A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
MUSCLE - Multiple PROTEIN sequences comparison by log-expectation at EBI
ProbCons - Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences
UCSC HMM Application
MEME suite - multiple EM for motif elicitation
WebLogo - sequence logo generation
MatchBox - suitable for finding and aligning conserved structural motives, in particular in protein core.
LAMA Block vs Block Searcher at Fred Hutchinson Cancer Research Center
MAFFT - Multiple Sequence Alignment based on fast Fourier transform at EBI
RevTrans takes a set of DNA sequences, virtually translates them, and aligns the peptide sequences