Alignement multiple


Artemis Comparison Tool

ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation.

Run Unix # Run Web #



Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks.

Remarque Citing Clustal: Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7.
Run Unix # clustalo --help Run Web #



Multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results.

Run Unix # clustalx (en mode graphique) ou clustalw2 (en mode ligne de commande)Run Web #



Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences.

Run Unix # GblocksRun Web #



KLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture, KLAST takes full advantage of recent multi-core personal computers without requiring any additional hardware devices.

Run Unix # Run Web #



7.164 2014-08-12DownloadDoc
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods.

Run Unix # mafft [options] input > outputRun Web #



Multiple Alignment of Conserved Regions in Genome Sequences

Run Unix # mauve Run Web #



Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

Remarque To cite Mugsy, use: Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes. Bioinformatics 2011 27(3):334-4
Run Unix # mugsy [-p output prefix] multifasta_genome1.fsa multifasta_genome2.fsa ... multifasta_genomeN.fsaRun Web #



MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.

Run Unix # mummer [options] Run Web #



MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.

Run Unix # muscle -in -out Run Web #



PROBCONS is a novel tool for generating multiple alignments of protein sequences. Using a combination of probabilistic modeling and consistency-based alignment techniques, PROBCONS has achieved the highest accuracies of all alignment methods to date. On the BAliBASE benchmark alignment database, alignments produced by PROBCONS show statistically significant improvement over current programs, containing an average of 7% more correctly aligned columns than those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W, and 14% more correctly aligned columns than those of DIALIGN.

Remarque Publications using the PROBCONS tool should cite:Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15:330-340.
Run Unix # probcons [OPTION]... [MFAFILE]...Run Web #



PyNAST: Python Nearest Alignment Space Termination tool PyNAST is a reimplementation of the NAST sequence aligner, which has become a popular tool for adding new 16s rDNA sequences to existing 16s rDNA alignments. This reimplementation is more flexible, faster, and easier to install and maintain than the original NAST implementation. PyNAST is built using the PyCogent Bioinformatics Toolkit. The first versions of PyNAST (through PyNAST 1.0) were written to exactly match the results of the original NAST algorithm. Beginning with the post PyNAST 1.0 development code, PyNAST no longer exactly matches the NAST output but is instead focused on getting better alignments. Users who wish to exactly match the results of NAST should download PyNAST 1.0.

Remarque PyNAST: a flexible tool for aligning sequences to a template alignment. J. Gregory Caporaso, Kyle Bittinger, Frederic D. Bushman, Todd Z. DeSantis, Gary L. Andersen, and Rob Knight. January 15, 2010, DOI 10.1093/bioinformatics/btp636. Bioinformatics 26: 266-267.
Run Unix # pynast [options] {-i input_fp -t template_fp} ou pynast -hRun Web #

Menu principal

Page | by Dr. Radut