Bioedit Sequence Alignment Editor
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 (42): ngsview Download |
Windows modeling tool that simplifies and speeds up the creation and maintenance of UML sequence diagrams, telecom/wireless call flow diagrams and process workflow diagrams. Sequence Diagram Editor performs automatic layout/formatting (across multiple pages if necessary) and supports additional...
Platforms: Windows
License: Shareware | Cost: $99.00 USD | Size: 6.82 MB | Download (559): Sequence Diagram Editor Download |
Algorithm::NeedlemanWunsch is a sequence alignment with configurable scoring. SYNOPSIS use Algorithm::NeedlemanWunsch; sub score_sub { if (!@_) { return -2; # gap penalty } return ($_[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 |
Jalview is used widely in a variety of web pages but is available as a general purpose alignment editor.
for WindowsAll
Platforms: Windows
License: Freeware | Download (440): Jalview Download |
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 |
A fast and reliable tool, written in Java 5, for generating professional UML sequence diagrams from text. Supports actors, con-/destructors, threads, broadcasts, notes, and fragments. Can serve as a Javadoc taglet. Exports PDF, (E)PS, SVG, PNG, ...
Platforms: Windows, Mac, Linux
License: Freeware | Size: 2.33 MB | Download (56): Quick Sequence Diagram Editor 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 |
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 |
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 |
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 |
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 |
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 |
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 |
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 (43): BACContigEditor 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 |
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 (52): JAligner 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 |
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 (43): NeedlemanWunsch Download |
A tool to compare two Protein Sequences and show similarities with the help of dotplot.
Platforms: Windows, Mac, Linux
License: Freeware | Size: 49.6 KB | Download (44): Sequence Alignment Download |