AMOS is a collection of tools for genome assembly
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.
Albion is a digital document archive presentation package. Features include a searchable database, an integrated spell checker, and automatic thumbnail generation. As native Perl as possible, the database/photos/search-function can be delivered on CD!
Symbolic Algebra using Perl
Algorithm::MatchingModel is a perl library for running match simulations and statistics for two-sided matching problems. It includes classes for a preference factory, algorithm plug-ins, and gathering statistics between rounds.
The system is designed for the automated analysis of high throughput sequencing data. At present Aped is focused on the analysis of data derived from Sanger and 454 sequencing. Additional functionality exists for SAGE and taxonomic profiling.
Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.
BigRedBin is a web-based tool designed to pre-process metabolomics data generated by a mass spectrometer in an attempt to increase the signal-to-noise ratio. This is accomplished by using information from multiple technical replicates.
A Perl module that provides methods for retrieving each and every field from a standard SwissProt file.
BioGraphNet is a 'sandbox' within BioMOBY, comprising a common standard and collection of services for sharing distributed protein-interaction network information. We now serve several network data types, and encourage others to participate.
Bobware tool suite is a set of small EDA tools which are useful in the design of integrated circuits. The suite contains a perl/tk script for region planning large ASICs (application specific integrated circuits.)
CODD is a tool for creating and analyzing statistical measures of "developer involvement" in free software projects.
The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects in OBO, OWL, and other commonly used ontology representation
A Perl object-oriented library for plotting graphs with Gnuplot.
Coati is a web development framework and API for genome databases that supports multiple database vendors and database schemas.
A collection of Perl modules and programs for bioinformatics. Design intention is to make most common, straight-forward tasks in computational biology as simple, and portable, as possible.
The Comprehensive Microbial Resource (CMR) is a free website used to display information on all of the publicly available, complete prokaryotic genomes.
DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).
A Perl script that interfaces with the Devantech USB to I2C interface adapter. This script allows a user to read and write as a master to the i2c bus as well as set or get the value of the io pins.
Testcalc is a CGI-based calculator for diagnostic test characteristics written in Perl that displays results both numerically and graphically.
EMBOSS explorer is a web-based graphical user interface to the EMBOSS suite of bioinformatics tools. It is written in Perl and is exceedingly simple to install, configure, maintain and use.
EVidenceModeler (aka EVM) combines ab initio gene predictions and spliced protein and transcript alignments into weighted consensus gene structure predictions.
Encode Arabic provides tools for encoding and decoding Arabic in Haskell, Python, Perl, or LaTeX. Interprets the ArabTeX notation to generate original orthography or phonetic transcription. Supports Buckwalter and other romanizations. Converts legacy byte encodings into Unicode. http://github.com/otakar-smrz/encode-arabic
an object-oriented API to access spatial data from Perl scripts, defines a set of classes and conventions to access spatial data independent of underlying file format or access method, based on OpenGIS Abstract Specification (see http://www.opengis.org)
GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior training.
The home of the Gene Ontology project on SourceForge, including ontology requests, software downloads, bug trackers, and much, much more.