| Version | MAJ | Artemis Comparison Tool | ||
| - | 2015-07-15 | Download | Doc |
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.
Remarque
| Run Unix # | Run Web # |
| Version | MAJ | BMGE | ||
| 1.1 | 2012-12-19 | Download | Doc |
BMGE (Block Mapping and Gathering with Entropy) is a program that selects regions in a
multiple sequence alignment that are suited for phylogenetic inference. BMGE selects
characters that are biologically relevant, thanks to the use of standard similarity matrices
such as PAM or BLOSUM. Moreover, BMGE provides other character- or sequenceremoval
operations, such stationary-based character trimming (that provides a subset of
compositionally homogeneous characters) or removal of sequences containing a too large
proportion of gaps. Finally, BMGE can simply be used to perform standard conversion
operations among DNA-, codon-, RY- and amino acid-coding sequences.
Remarque
| Run Unix # BMGE ou BMGE -? | Run Web # |
| Version | MAJ | clustal-omega | ||
| 1.1.0 | 2012-07-17 | Download | Doc |
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 # |
| Version | MAJ | clustalx | ||
| 2.1 | 2013-12-29 | Download | Doc |
Multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results.
Remarque
| Run Unix # clustalx (en mode graphique) ou clustalw2 (en mode ligne de commande) | Run Web # http://www.ebi.ac.uk/Tools/msa/clustalw2/ |
| Version | MAJ | dialign | ||
| 2.2.1 | 2005-12-06 | Download | Doc |
sDIALIGN is a software program for multiple alignment developed by Burkhard Morgenstern et al. While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing whole segments of the sequences. No gap penalty is used. This approach is especially efficient where sequences are not globally related but share only local similarities, as is the case with genomic DNA and with many protein families.
Remarque
| Run Unix # dialign | Run Web # |
| Version | MAJ | Gblocks | ||
| 0.91b | 2006-07-19 | Download | Doc |
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.
Remarque
| Run Unix # Gblocks | Run Web # |
| Version | MAJ | genehunter | ||
| 2.1_r2 | 2002-09-27 | Download | Doc |
Multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction
Remarque
| Run Unix # gh | Run Web # |
| Version | MAJ | Klast | ||
| 4.4 | 2015-04-24 | Download | Doc |
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.
Remarque
| Run Unix # | Run Web # |
| Version | MAJ | mafft | ||
| 7.164 | 2014-08-12 | Download | Doc |
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods.
Remarque
| Run Unix # mafft [options] input > output | Run Web # |
| Version | MAJ | mango | ||
| 0.1.0 | 2008-02-12 | Download | Doc |
Multiple Alignment with N Gapped OligossMANGO: A NEW APPROACH TO MULTIPLE SEQUENCE ALIGNMENT
Remarque Please use four scripts provided:smang8: MANGO with 8 seeds, without refinement;smang8r: MANGO with 8 seeds, with refinement;smang90: MANGO with 90 seeds, without refinement;smang90r: MANGO with 90 seeds, with refinement;s
| Run Unix # mang8 ; mang8r ; mang90 ; mang90r | Run Web # |
| Version | MAJ | mauve | ||
| 2.4.0 | 2015-01-07 | Download | Doc |
Multiple Alignment of Conserved Regions in Genome Sequences
Remarque
| Run Unix # mauve | Run Web # |
| Version | MAJ | Mugsy | ||
| 1.2.3 | 2013-07-19 | Download | Doc |
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.fsa | Run Web # |
| Version | MAJ | multalin | ||
| 5.4.1 | 2002-04-04 | Download | Doc |
This software will allow you to align simultaneously several biological sequences.
Remarque
| Run Unix # ma | Run Web # http://www.toulouse.inra.fr/multalin.html |
| Version | MAJ | mummer | ||
| 3.23 | 2015-03-02 | Download | Doc |
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.
Remarque
| Run Unix # mummer [options] | Run Web # |
| Version | MAJ | muscle | ||
| 3.8.31 | 2014-08-24 | Download | Doc |
MUSCLE stands for MUltiple Sequence Comparison by Log-Expectation.
Remarque
| Run Unix # muscle -in | Run Web # |
| Version | MAJ | probcons | ||
| 1.12 | 2010-04-11 | Download | Doc |
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 # |
| Version | MAJ | pynast | ||
| 0.1 | 2012-07-23 | Download | Doc |
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 -h | Run Web # |
| Version | MAJ | SLICEMBLER | ||
| - | 2015-01-26 | Download | Doc |
SLICEMBLER is an iterative meta-assembler that takes advantage of the whole
dataset, and significantly improves the final quality of the assembly.
SLICEMBLER partitions the input data into optimal-sized “slices” and uses
a standard assembly tool (e.g., Velvet, SPAdes, IDBA, Ray) to assemble each
slice individually. SLICEMBLER uses majority voting among the individual
assemblies to identify long contigs that can be merged to the consensus
assembly. It extracts high-quality contigs from the slice assemblies, and
prevents contigs containing mis-joins and calling errors to be included in
the final assembly.
SLICEMBLER has been designed and developed at the algorithm and computational biology lab. , university of California, Riverside.
Remarque
| Run Unix # slicembler.py -r | Run Web # |
| Version | MAJ | ssu-align | ||
| 0.1.1 | 2016-07-01 | Download | Doc |
SSU-ALIGN is a software package for identifying, aligning, masking and visualizing archaeal 16S, bacterial 16S and eukaryotic 18S small subunit ribosomal RNA (SSU rRNA) sequences. It includes and uses the Infernal software package for generating alignments based on the conserved secondary structure and sequence of SSU rRNA. SSU-ALIGN extends Infernal to make it easier for users to generate large-scale alignments of up to millions of SSU rRNA sequences that will ultimately be used as input to phylogenetic inference methods. (SSU-ALIGN is not capable of inferring phylogenetic trees itself.) Large SSU rRNA sequence datasets are commonly generated by environmental sequencing survey studies that use SSU rRNA as a phylogenetic marker of species in the environment being studied. While designed primarily for these SSU-based studies, SSU-ALIGN is a general tool that can be used to generate alignments of any type of structural RNA, including large subunit ribosomal RNA (LSU rRNA).
Remarque How to cite SSU-ALIGN SSU-ALIGN does not yet have an associated publication, so please cite the INFERNAL software publication ((Nawrocki et al., 2009a)) if you find the package useful for work that you publish. Additionally, because SU-ALIGN’s seed alignments were derived from the comparative rna website we ask that you cite that database as well: (Cannone et al., 2002).
| Run Unix # | Run Web # |
| Version | MAJ | T-Coffee | ||
| 11.00.8cbe486 | 2015-04-07 | Download | Doc |
T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.
Remarque
| Run Unix # t_coffee sequence_file | Run Web # |
