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Multiple Sequence Alignment freeware
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Multiple Sequence Alignment

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Released: November 04, 2012  |  Added: November 04, 2012 | Visits: 260

UGENE UGENE is a comprehensive genome analysis suite that features multiple sequence alignment and a complex HMM builder and search module. for WindowsAll Platforms: Windows

License: Freeware Download (59): UGENE Download

Added: August 21, 2013 | Visits: 258

FSA For Linux FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Platforms: *nix

License: Freeware Size: 9.61 MB Download (22): FSA For Linux Download

Released: August 07, 2012  |  Added: August 07, 2012 | Visits: 214

MacGDE for Mac OS A set of programs for multiple sequence alignment and analysis. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. The system supports several data types, nucleic and amino acid sequences, text, and masking... Platforms: Mac

License: Freeware Size: 42.8 MB Download (28): MacGDE for Mac OS Download

Released: June 27, 2012  |  Added: June 27, 2012 | Visits: 286

FSA FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences. Platforms: Mac, BSD, Linux

License: Freeware Size: 9.61 MB Download (29): FSA Download

Added: February 01, 2010 | Visits: 957

Algorithm::NeedlemanWunsch Algorithm::NeedlemanWunsch is a sequence alignment with configurable scoring. SYNOPSIS use Algorithm::NeedlemanWunsch; sub score_sub { if (!@_) { return -2; # gap penalty } return ($_[0] eq $_[1]) ? 1 : -1; } my $matcher = Algorithm::NeedlemanWunsch->new(&score_sub); my $score =... Platforms: *nix

License: Freeware Size: 10.24 KB Download (86): Algorithm::NeedlemanWunsch Download

Added: January 26, 2010 | Visits: 674

NeoBio NeoBio project consists of Bioinformatics algorithms in Java. What algorithms? The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment).... Platforms: *nix

License: Freeware Size: 102.4 KB Download (91): NeoBio Download

Added: September 27, 2013 | Visits: 212

MSAProbs For Linux MSAProbs is an open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. Platforms: *nix

License: Freeware Size: 931.84 KB Download (16): MSAProbs For Linux Download

Added: June 23, 2013 | Visits: 229

MUMmerGPU MUMmerGPU is a high-throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. It aligns sequences in parallel on the video card to accelerate the widely used serial CPU program MUMmer. Platforms: *nix

License: Freeware Size: 51.2 KB Download (16): MUMmerGPU Download

Released: September 09, 2012  |  Added: September 09, 2012 | Visits: 294

Geneious for Mac OS An automatically-updating library of genomic and genetic data; that provides a fully integrated, visually-advanced toolset for - Sequence alignment and phylogenetics - Sequence analysis, Contig assembly, - primers, restriction analysis - BLAST. Protein structure viewing, NCBI, UniProt, Pubmed... Platforms: Mac

License: Freeware Size: 77 MB Download (28): Geneious for Mac OS Download

Released: October 14, 2012  |  Added: October 14, 2012 | Visits: 249

BACContigEditor BACContigEditor is a simple sequence alignment editing tool, written in Java. It is originally developed for finishing BAC shotgun sequencing projects, but the program could be easily extended to the whole genome project. Platforms: Windows, Mac, Linux

License: Freeware Size: 867.54 KB Download (27): BACContigEditor Download

Released: August 23, 2012  |  Added: August 23, 2012 | Visits: 248

BiasViz BiasViz is a Java applet for visualization of amino acid bias in multiple sequence alignments. Platforms: Windows, Mac, Linux

License: Freeware Size: 130.91 KB Download (27): BiasViz Download

Released: August 12, 2012  |  Added: August 12, 2012 | Visits: 221

JAligner JAligner is an open source Java implementation of the dynamic programming algorithm Smith-Waterman with Gotoh's improvement for biological local pairwise sequence alignment with the affine gap penalty model. Platforms: Windows, Mac, Linux

License: Freeware Size: 162.36 KB Download (28): JAligner Download

Released: September 13, 2012  |  Added: September 13, 2012 | Visits: 269

NeedlemanWunsch Global optimal sequence alignment using the Needleman-Wunsch algorithm. Aligns DNA, RNA, protein sequence and more! See our sister project local alignment using Smith-Waterman: http://sourceforge.net/projects/smithwaterman/ Platforms: Mac, BSD, Linux

License: Freeware Size: 36.87 KB Download (27): NeedlemanWunsch Download

Released: June 08, 2012  |  Added: June 08, 2012 | Visits: 290

Sequences studio Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet. Platforms: Windows, Mac, Linux

License: Freeware Size: 96.58 KB Download (27): Sequences studio Download

Released: October 16, 2012  |  Added: October 16, 2012 | Visits: 234

SmithWaterman An implementation of the Smith-Waterman local sequence alignment algorithm. See our sister project global alignment using Needleman-Wunsch: http://sourceforge.net/projects/needlemanwunsch/ Platforms: Mac, BSD, Linux

License: Freeware Size: 43.02 KB Download (29): SmithWaterman Download

Added: November 19, 2013 | Visits: 270

SAM Tools SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: * Is flexible enough to store all the alignment information generated by various alignment programs; * Is simple enough to be easily generated by alignment... Platforms: Mac

License: Freeware Size: 368.64 KB Download (16): SAM Tools Download

Added: November 30, 2013 | Visits: 179

ngsview NGSView is a generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. Platforms: *nix

License: Freeware Size: 77.7 MB Download (24): ngsview Download

Added: March 13, 2010 | Visits: 730

App::Session App::Session can represents a sequence of multiple events perhaps executed in separate processes. SYNOPSIS # ... official way to get a Session object ... use App; $session = App->context(); $context = $session->session(); # get the session # any of the following named parameters may be... Platforms: *nix

License: Freeware Size: 73.73 KB Download (73): App::Session Download

Added: July 27, 2010 | Visits: 435

AlignAid AlignAid is a Perl module that easily run sequence alignments locally or on a cluster. SYNOPSIS use AlignAid; # create an AlignAid object # a single, locally run blast job is the default my $job = AlignAid->new( db => my_blast_db, dir => $dir, fasta => my_query.fa, prog_args => V=20... Platforms: *nix

License: Freeware Size: 348.16 KB Download (72): AlignAid Download

Released: October 24, 2012  |  Added: October 24, 2012 | Visits: 446

BlastViewer BlastViewer provides an interactive graphical user interface for the analysis of the reports produced by the BLAST sequence database search system. BlastViewer is an easy to use software designed for everyday biological sequence analysis relying on BLAST. It allows an easy visualisation and... Platforms: Mac, Java 1.5 or later

License: Freeware Size: 7.5 MB Download (34): BlastViewer Download

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