Multiple Sequence Alignment
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 (467): UGENE Download |
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 (39): FSA For Linux Download |
Phylo-mLogo is an interactive multiple-logo visualization tool for large-number sequence alignments which allows the user to visualize the global profile of whole multiple sequence alignment and to hierarchically visualize homologous logos of each clade simultaneously.
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 1.97 MB | Download (37): Phylo-mLogo Download |
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 (49): MacGDE for Mac OS Download |
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 (53): FSA Download |
MSA2SNP is a tool for mining SNP sites in multiple sequence alignment (MSA). This tool inherits the easy-to-use interface from MEGA4 Explorer with advance data presentation. MSA2SNP lets you visualize alignments and import from CLUSTAL program directly.
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 143.36 KB | Download (48): MSA2SNP Download |
SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView reads and writes various file formats of DNA and protein sequences and of phylogenetic trees. SeaView drives programs muscle or clustalw for multiple sequence alignment, and...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 3.71 MB | Download (45): SeaView fopr Mac Download |
The classic genotyping approach has been based on phylogenetic analysis, starting with a multiple sequence alignment. Genotypes are then established by expert examination of phylogenetic trees. However, such methods are suboptimal for a rapidly growing dataset, because they require significant...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 25.45 MB | Download (38): CompleteCompositionVectorCLI Download |
SinicView: A visualization environment for comparisons of multiple nucleotide sequence alignment tools. Background Deluged by the rate and complexity of completed genomic sequences, the need to align longer sequences becomes more urgent, and many more tools have thus been developed. In the...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 3.92 MB | Download (42): SinicView Download |
Algorithm::NeedlemanWunsch is a sequence alignment with configurable scoring. SYNOPSIS use Algorithm::NeedlemanWunsch; sub score_sub { if (!@_) { return -2; # gap penalty } return ($_[0] eq $_[1]) ? 1 : -1; } my $matcher = Algorithm::NeedlemanWunsch->new(&score_sub); my $score =...
Platforms: *nix
License: Freeware | Size: 10.24 KB | Download (105): Algorithm::NeedlemanWunsch Download |
Gene Inspector is a unique combination of a versatile electronic laboratory research notebook and a comprehensive sequence analysis product. Using GI, the user has the ability to define an entire 'suite of analyses' that can be performed each time they (or anyone in the lab) has a new sequence,...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Download (102): Gene Inspector Download |
MacVector... Researchers who want a simple but comprehensive desktop sequence analysis application continually turn to MacVector, the leading sequence analysis package for the Macintosh. MacVector provides sequence editing, primer design, Internet database searches, protein analysis, sequence...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Download (126): MacVector Download |
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 (109): NeoBio Download |
When a large number of samples is analyzed by mass spectrometry instrument, a common issue is the multiple spectra peaks alignment. In fact, the statistical analysis generally requires a data matrix, easily to import from a file to the software. Furthermore, in a multiple mass spectrometry...
Platforms: Matlab
License: Shareware | Cost: $0.00 USD | Size: 30.72 KB | Download (39): Multiple Peaks Alignment for Mass Spectrometry Download |
ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Size: 66.56 KB | Download (51): ZORRO Download |
Gene Construction KitO brings intuitive productivity to the molecular biology researcher's MAC, allowing effortless manipulation of DNA - either graphically or as sequence text. GCK eliminates tedious examination of sequence data by automatically identifying ORF's and silent mutations, and easily...
Platforms: Mac
License: Demo | Cost: $0.00 USD | Download (123): GCK Download |
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 (34): MSAProbs For Linux Download |
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 (33): MUMmerGPU Download |
Search oligonucleotide in multiple sequence files. Primer Validator is a scientific utility which allows researchers to verify whether the designed primer is unique for the gene of interest or not. It will be useful if that gene is a member of a large superfamily. In addition, researchers may...
Platforms: Mac
License: Shareware | Cost: $0.00 USD | Download (103): Primer Validator Download |
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 (58): Geneious for Mac OS Download |