- ad The ARB Project
- arb-home.de
- A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.
- Cytoscape
- www.cytoscape.org
- Open source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. It is also a general platform for complex network analysis and visualization.
4.2
(si*)
>600
>80
6
- Geneious
- www.geneious.com
- This research software is designed for biologists and not computer scientists. It combines all the major DNA and protein sequence analysis tools into one software solution.
4.2
(si*)
>1790
<5
6
- EMBOSS
- emboss.sourceforge.net
- The European Molecular Biology Open Software Suite. An open source project started by the EMBnet community in order to replace proprietary systems like GCG.
4.2
(si*)
>10
>10
6
- Generic Model Organism Database Construction Set
- gmod.org
- Collection of interoperable open source software components for visualizing, annotation and managing data.
4.0
(si*)
>60
<5
6
- HMMER: Biosequence Analysis
- hmmer.janelia.org
- A tool used to build HMMs from multiple alignments and calculate e-scores. [GPL]
4.0
(si*)
>30
>30
6
- Unipro UGENE: Integrated Bioinformatics Tools
- ugene.unipro.ru
- Free cross-platform bioinformatics software package for DNA and protein sequence analysis.
4.0
(si*)
>100
>50
5
- JAligner
- jaligner.sourceforge.net
- Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
3.9
(si*)
<5
<10
5
- Premier Biosoft International
- www.premierbiosoft.com
- Developers of software for real time PCR primer design, TaqMan, molecular beacons, DNA microarray analysis, drawing restriction plasmid maps, gateway cloning experiments, protein interaction network and functional genomics.
3.8
(si*)
>30
-
5
- PhyloSort
- phylosort.sourceforge.net
- A Java tool to sort phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
3.7
(si*)
-
-
3
- sys-bio.org
- sbw.kgi.edu
- Software for simulating metabolic, signal and genetic networks. Home of SBW, Jarnac, JDesigner and winSCAMP.
3.7
(si*)
<5
-
5
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