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  2D HF

  This is an extension to the standard 2D HF package (A Numerical Hartree-Fock Program for Diatomic Molecules by Jacek Kobus, Leif Laaksonen and Dage Sundholm) that adds some extra functionality.

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  Assembly of mixed genomes

  Scripts used to assemble and deconvolute mixed mitochondrial genomes.

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  BIOperl Scripts for PHylogenetic Analyse

  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.

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  BODE: Bioinformatics ODds and Ends

  A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).

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  BibGlimpse MEDLINE Retriever

  Literature management tools typically require that bibliography is typed in by hand for each PDF reprint added. The BibGlimpse retriever presented here can automatically find Medline entries for arbitrary PDFs ( http://bioinf.boku.ac.at/bibglimpse ).

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  BioInfoServ Project

  The ideal Operation System, BioInfoServOS, which is a specially customised system for scientists handling and analysing biological data, but also for easy use of daily official business handing, has been distributed. Download it from www.bioinfoserv.org

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  Cscape (Cancer Landscape)

  Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways.

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  DIY Genomics

  DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

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  Disco

  Disco (DIStribution of COnformations) is a software package for the estimation of solution conformations of organic molecules. It is rewritten form of NAMFIS method and can be used with the input files generated by Janocchio.

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  GPSR: A bioinformatics suite

  GPSR is a resource for genomics, proteomics and systems biology. The aim of this project is to build comprehensive resources in the field of bioinformatics.

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  Gaussian Output Tools

  Gaussian Output Tools is a package of simple scripts to extract data from Gaussian output files.

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  Generic Genetic Studies Database

  The Generic Genetic Studies Database (GGSD) is a web-based, relational database driven data management software package for the management of large scale genetic studies.

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  Gvib

  GVIB is a user friendly package for vibrational analysis. Given a molecular geometry, it will calculate vibrational frequencies and intensities using anharmonic internuclear potential.

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  HOPPscore - Protein Structure Quality

  HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.

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  IndelExtractor

  IndelExtractor is a GUI and command-line application written in Perl that generates various molecular sequence alignment masks, including one to make identification and removal of Indels and their surrounding ambiguous alignment quick and simple.

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  IsoFind

  Project to create a set of algorithms which will identify and isolate mRNA isoforms through primer design for RT-PCR techniques.

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  MAVEN

  Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.

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  MBPT (Molecular Biology Perl Tools)

  MBPT (Molecular Biology Perl Tools) is a toolkit for Molecular Biologists that focuses mainly on sequence analysis/representation, as well as format conversions.

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  NMRC Genomics Software

  Bioinformatics tools and applications for the analysis of genomic sequence data.

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  Parentheses Classifier

  The Parenthesis Classifier takes the contents of a set of parentheses and classifies it into one of several categories. It includes a parenthesized-data extractor and the classifier.

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  PhosCalc

  A perl command line tool for calculating likelihood of phosphorylation sites in peptides from mass spec data

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  Process_hits

  A fast efficient way of dealing with large amounts of Blast or Repeatmasker data.

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  ProteoConnections

  ProteoConnections is a bioinformatics platform tailored to address the pressing needs of proteomic analyses. Organise identifications, evaluate the the acquired dataset and accelerate biological interpretation using bioinformatics applications.

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  RNA2.5D

  RNA2.5D will be a novel method of predicting the secondary structure of small RNAs (upto 200nt) using tertiary structure information.

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  SASHIMI

  The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to our open mzXML format.

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