Needle: Pairwise Alignment Algorithms: you can obtein Identity and Similarity
BLAST (Japan): you can do direct clustalW analysis
EMBOSS Pairwise Alignment Algorithms: you can obtein Identity and Similarity
BLAST (NCBI): Basic Local Alignment Search Tool. finds regions of similarity between biological sequences
SAM: UCSC's Sequence Alignment and Modeling System
SIM: Alignment Tool for protein sequences
ESPRIPT: Easy Sequencing in PostScript: alignment and secondary structure scheme for publications. [###TOP##]
Tcoffe: A Program for Multiple Sequence Alignment
clustalO:Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments
EMBL-EBI:Multiple Sequence Alignment (MSA)
AMAS Server: Analyse Multiply Aligned Sequences
Barton lab:Multiple Sequence Alignment and Analysis
## ESPRIPT: Easy Sequencing in PostScript: alignment and secondary structure scheme for publications
RAPIDO is an algorithm for the 3D alignment of protein structures. In order to align your protein structures:output =RMSD. you can upload multiples PDB files (tarball.tgz <list-of-pdb-files>).
RaptorX Structure Alignment - protein pairwise and/or multiple structure alignment
Strap: intuitive Editor for annotated multiple Sequence and Structure Alignments
TM-align: A protein structure alignment algorithm using TM-score rotation matrix
Online Structure Alignment Resources (list)
pairwise DaliLite server: superimpose two particular structures
T-RMSD (Tree based on Root Mean Square Deviation): is a distance RMSD (dRMSD) based method which generate Structural Trees (analogue to phylogenetic tree) to determine fine-grained structural variations associated with a given Multiple Sequence Alignment. It is part of the T-Coffee distribution.
Stamp: STAMP is a suite of programs for the comparison and alignment of protein three dimensional structures.
SSAP: The SSAP server allows users to compare the structures of two proteins and view the subsequent structural alignment
MUSCLE:protein multiple sequence alignment software
MAFFT ver.5 - a multiple sequence alignment program
SINCRIS software, Stamp: structural alignment
Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion.
PFAAT:Protein Family Alignment Annotation Tool
XCED - a multiple sequence alignment editor
multiple sequence alignment: Interactive Editor STRAP
BioEdit is a biological sequence alignment editor written for Windows 95/98/NT/2000/XP.
SeaView is a graphical multiple sequence alignment editor developped by Manolo Gouy. SeaView is able to read and write various alignment formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE). It allows to manually edit the alignment, and also to run DOT-PLOT or CLUSTALW/MUSCLE programs to locally improve the alignment.
SequenceJuxtaposer: Fluid Navigation For Large-Scale Sequence Comparison In Context
ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences
Geneious Pro: is an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information, publications, etc.
Alignment visualization tools server: These tools should help you with preparation of publication-quality pictures of your alignment. Description ot the server and examples of its use are in the help page.
WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible
MoRAine is a tool for the reannotation of transcription factor binding motifs and the creation of sequence logos