Pairwise Sequence Alignment
- Needle@EBI – Needleman-Wunsch global sequence alignment tool.
- BLAST@NCBI – Alignment tool to find regions of similarity between biological sequences.
- Stucture Alignment – Pairwise structure alignment tool at PDB.
- Water@EBI – For local sequence alignment based on Smith-Waterman algorithm.
- Dotlet@SIB – Sequence comparison with dot plot.
Multiple Sequence Alignment
- COBALT@NCBI – Constraint-based Multiple Alignment Tool. Computes a multiple protein sequence alignment using conserved domain and local sequence similarity information.
- Clustal Omega@EBI – Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments.
- Muscle@EBI – MUltiple Sequence Comparison by Log- Expectation. Multiple sequence comparison with better average accuracy and speed.
- MAFFT@EBI – Multiple Alignment using Fast Fourier Transform. High speed multiple sequence alignment program.
- KALIGN@EBI – A fast and accurate multiple sequence alignment algorithm.
- T-Coffe@EBI – Multiple alignment program that allows to combine results obtained with several alignment methods.
- STRAP – Intuitive Editor for annotated multiple Sequence and Structure Alignments
- Weblogo – A web based application designed to easily generate sequence logos .
Sequence Similarity Search
- NCBI – Sequence similarity seacrh programs at NCBI including PSI-BLAST and PHI-BLAST, etc.
- EBI – Sequence similarity search programs at EBI including FASTA, BLAST and SSEARCH, GGSearch, GLSearch, HMMER.
- BLAST/BLAT@Ensembl – Sequence similarity search tool at Ensembl.
- BLAT@UCSC – Sequence similarity search program available at UCSC genome browser.
- Sanger BLAST – Sanger Genome Sequencing Projects BLAST.