Bioinformatics
- 141
- DNPTrapper
- A Linux assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions.
- 142
- GeneRunner
- A fairly old Windows sequence analysis tool for everyday lab use. Formerly a commercial product.
- 143
- Geneious
- 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.
- 144
- Genome-tools Web Interface
- Genome-tools provides flexible tools and a simple API for genomic sequence processing on genomes published in the standard Genbank format.
- 145
- Gints
- Object-oriented regulation network simulator written in Java. Includes downloadable software and documentation. The site is in French and English.
- 146
- JAligner
- Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
- 147
- MARBL
- MARBL is a free (GPL) system to index the text portions of GenBank and associated NLM abstracts. Based on Mumps and the MDH.
- 149
- NEXML: Phylogenetic Data in xml
- Exchange standard for representing phylogenetic data, inspired by the commonly used NEXUS format but more robust and easier to process.
- 151
- PhyloSort
- 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.
- 152
- Premier Biosoft International
- Developers of software for real time PCR primer design, TaqMan, molecular beacons, SYBR green, FRET, DNA microarray analysis, restriction cloning, plasmid maps, gateway cloning, protein interaction network and functional genomics.
- 153
- RGBG Analyzer
- Commercial software to analyses the red, green, blue, and gray color values of user-selected areas of images in gif, tiff, bmp, jpeg format. Windows 2000 and XP.
- 154
- SMSD (Small Molecule Subgraph Detector)
- SMSD is a Java based software library for calculating Maximum Common Subgraph (MCS) between small molecules. This will aid finding resemblances between two molecules and is also used for screening drug-like compounds.
- 155
- SeWeR
- An integrated portal for common web-based bioinformatics services. Built in Javascript as a standalone browser application.
- 156
- Seqtools
- Commercial Windows software for batch handling and analysis of nucleotide and protein sequences.
- 157
- Sequence Analysis
- A freeware Java application that does many standard types of DNA and protein sequence analysis tasks.
- 159
- The ARB Project
- 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.