Alignment with affine gap penalties

NW-align is simple and robust alignment program for protein sequence-to-sequence alignments based on the standard Needleman-Wunsch dynamic programming algorithm. The mutation matrix is from BLOSUM62 with gap openning penalty=-11 and gap extension penalty=-1. The source code of this program can be downloaded at the bottom of this page, which can be easily modified for different purposes. A Java code using the standard Smith-Waterman algorithm for local sequence alignment was recently added in the page as well.

Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.

Sequence alignment algorithms are widely used to infer similarirty and the point of differences between pair of sequences. FOGSAA is a fast Global alignment algorithm. It is basically a branch and bound approach which starts branch expansion in a greedy way taking the symbols from the given pair of sequences (protein or nucleotide) and results in an optimal alignment faster than conventional dymanic programming techniques. It is also better than the heuristic methods with respect to alignment quality. Obtaining high quality sequence alignment as well as minimizing the running time, is a real challenge in bioinformatics. FOGSAA is an invention in this direction.

T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle) into one unique alignment (M-Coffee). T-Coffee can align Protein, DNA and RNA sequences. It is also able to combine sequence information with protein structural information (3D-Coffee/Expresso), profile information (PSI-Coffee) or RNA secondary structures.

Gap considers all possible alignments and gap positions between two sequences and creates a global alignment that maximizes the number of matched residues and minimizes the number and size of gaps. A scoring matrix is used to assign values for symbol matches. In addition, a gap creation penalty and a gap extension penalty are required to limit the insertion of gaps into the alignment. Gap uses the alignment method of Needleman and Wunsch (J. Mol. Biol. 48; 443-453 (1970)) that has been shown to be equivalent to Sellers (SIAM J. of Applied Math 26; 787-793 (1974))

Module pairwise2 is a Biopython module that implements pairwise sequence alignment using a dynamic programming algorithm.

This module provides a python module and a command-line interface to do global- sequence alignment using the Needleman-Wunsch algorithm. It uses cython and numpy for speed.

Bioinformatics Toolbox™ provides algorithms and apps for Next Generation Sequencing (NGS), microarray analysis, mass spectrometry, and gene ontology. Using toolbox functions, you can read genomic and proteomic data from standard file formats such as SAM, FASTA, CEL, and CDF, as well as from online databases such as the NCBI Gene Expression Omnibus and GenBank®. You can explore and visualize this data with sequence browsers, spatial heatmaps, and clustergrams. The toolbox also provides statistical techniques for detecting peaks, imputing values for missing data, and selecting features.

needle is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Alignment:Global" command group(s). It uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length.