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  Avogadro

  Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.

  1,571 weekly downloads
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  Bowtie

  Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.

  1,419 weekly downloads
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  Generic Model Organism Database Project

  GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.

  210 weekly downloads
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  MUMmer

  MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

  166 weekly downloads
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  Gene Ontology

  The home of the Gene Ontology project on SourceForge, including ontology requests, software downloads, bug trackers, and much, much more.

  104 weekly downloads
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  Perl Data Language

  The PDL module gives standard perl the ability to COMPACTLY store and SPEEDILY manipulate the large N-dimensional data sets that are the bread and butter of scientific computing.

  60 weekly downloads
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  One-Wire Weather

  Oww (One-Wire Weather) is a server and client for Dallas Semiconductor / AAG 1-wire weather station kits.

  18 weekly downloads
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  Yet Another Prolog

  The Yap Prolog System is a ISO-compatible high-performance Prolog compiler. Yap is widely considered one of the fastest available Prolog systems. Yap supports coroutining, CLP(QR), CHR, and depth-bound search. Tabling and parallelism are in development.

  16 weekly downloads
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  Ramugen : Random Music Generator

  Ramugen is a music application which assists in / automates composition along stochastic/indeterminate lines. Comes as a Win32 desktop application and a Borland Delphi component-package. Open Source : full source-code and documentation provided. Very fle

  18 weekly downloads
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  TGI Clustering Tool

  A software solution for clustering large EST/mRNAs datasets.

  15 weekly downloads
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  SPM surfrend

  SPM surfrend toolbox is a suite of scripts that add surface-based rendering capabilities to SPM99/2 generated statistical maps.

  8 weekly downloads
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  Selective File Dumper

  This is a computer forensics useful tool written in bash script for Linux systems. It's fast and selective, you can retrieve all the files of the file type you choose with only one tool referenced, deleted and unallocated in very fast way.

  8 weekly downloads
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  Simple 2D Windows Grapher

  An efficient 2D Simple Graphing program for windows, perfect for plotting collected data incorporating features of cricket graph which allow you to apply a function to all your data. Regression Lines for data.

  8 weekly downloads
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  Wordcorr

  Data management for comparative linguistics

  2 weekly downloads
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  DAGchainer

  DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG).

  4 weekly downloads
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  IDEA

  IDEA (Interactive Display for Evolutionary Analyses) augments PAML with a graphical interface, phylogeny reconstruction using PhyML or PHYLIP, convenient and efficient parallel processing and visualizations.

  6 weekly downloads
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  CloudBurst

  CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

  5 weekly downloads
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  ergatis

  Ergatis is a web-based utility used to create, run, and monitor reusable computational analysis pipelines, utilizing the Workflow engine. It contains pre-built components for common bioinformatics analysis tasks.

  5 weekly downloads
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  Manatee

  Manatee is a web-based gene evaluation and genome annotation tool. Manatee can store and view annotation for prokaryotic and eukaryotic genomes.

  4 weekly downloads
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  Encode Arabic

  Implementations for encodings of Arabic, in Haskell and Perl. Support for ArabTeX, Buckwalter, UTF and other encodings. Interpretable notations generating original orthography and/or phonetic transcriptions.

  2 weekly downloads
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  pteros

  Pteros is the C++ library for custom molecular modeling and simulations codes designed for researchers, not for C++ gurus. Provides facilities for PDB, XTC and TRR files IO, powerful selections, geometry transformations, RMSD fitting and alignment, etc.

  2 weekly downloads
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  Diagnostic Test Calculator

  Testcalc is a CGI-based calculator for diagnostic test characteristics written in Perl that displays results both numerically and graphically.

  3 weekly downloads
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  Coding Explorer

  Numerically estimate an efficiency of code construction algorithms. Randomly generate n binary words of length m with minimum Hamming distance d and create a prefix code (= retrieval tree) from them. Based on PhD work.

  2 weekly downloads
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  Mister Model

  Mister Model is a code generation system. It takes a UML model expressed as XMI and generates source code specifically designed to work in a cross-platform web service environment. It fixes the legendary 'Serialization Failed' messages in web services

  2 weekly downloads
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  Systems Biology Ontology

  The Systems Biology Ontology project (SBO) goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling.

  2 weekly downloads

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