228 projects tagged "Bioinformatics"

Download Website Updated 19 Apr 2006 DNALinux

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Pop 62.94
Vit 2.98

DNALinux is a live Linux distribution with bioinformatics software preloaded. It is for people who find it hard to install EMBOSS, Primer3, BLAST, and other bioinformatics software or who want to have a test system for class or demonstration purposes.

Download Website Updated 19 Apr 2004 Py_ContigViewer

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Pop 10.68
Vit 1.74

Py_ContigViewer is a contig viewer, a stand alone cross-platform desktop application that uses CAP3 alignments to graphically display and validate candidate SNPs and InDels. It also simplifies PCR oligo design in an interactive mode. The extended mode provides the display of BLAST hits of annotated sequences with intron positions for the selected contig. Py_ContigViewer works in conjunction with DIS (Deletion, Insertion, Substitution) SNP discovery pipeline at http://www.atgc.org/SNP_Discovery/.

Download Website Updated 29 Sep 2007 SoundRuler

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Pop 48.40
Vit 2.14

SoundRuler is a tool for acoustic analysis, graphing, and teaching. It interactively recognizes and measures 35 temporal and spectral properties of each sound in a file. It also features several measurement, graphing, and didactic modules.

Download No website Updated 31 Mar 2004 jgram

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Pop 19.39
Vit 1.00

jgram is a simple markov-chain library suitable for building rudimentary n-gram representations of sequences of any Java objects. It has an extensible scoring mechanism and a generator for traversing a random path through n-gram states based on transition score.

No download Website Updated 07 Sep 2005 Vigyaan

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Pop 27.75
Vit 1.52

Vigyaan is an electronic workbench for bioinformatics, computational biology, and computational chemistry. It is a Linux-live CD containing all the required software to boot the computer with ready to use modeling software. It includes Artemis, Bioperl, BLAST (NCBI-tools), ClustalX, Cn3D, EMBOSS tools, Garlic, GROMACS, Ghemical, GNU R, Gnuplot, GIMP, ImageMagick, JMol, MPQC, NJPlot, Open Babel, Octave, PSI3, PyMOL, Rasmol, Raster3D, SMILE, TINKER, XDrawChem, Xmgr, and Xfig.

No download Website Updated 26 Mar 2008 ProActive

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Pop 41.95
Vit 2.22

ProActive is a Java library for parallel, distributed, and concurrent computing as well as mobility and security in a uniform framework. It provides a comprehensive API and a graphical interface and is based on an Active Object pattern, a uniform way to encapsulate a remotely accessible object, a thread as an asynchronous activity, an actor with its own script, a server of incoming requests, a mobile and secure agent, and a component with server and client interfaces. It simplifies the programming of applications distributed over a LAN, clusters, an intranet, or Internet GRIDs.

Download Website Updated 28 Feb 2006 CoaSim

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Pop 42.31
Vit 5.96

CoaSim is a tool for simulating the coalescent process with recombination and gene conversion under the assumption of exponential population growth. It efficiently constructs the ancestral recombination graph for a given number of individuals and uses this to simulate samples of SNP and micro satellite haplotypes/genotypes. The generated sample can afterwards be separated in cases and controls, depending on the states of selected individual markers. The tool can accordingly also be used to construct cases and control data sets for association studies.

Download Website Updated 03 Jan 2006 Staden Package

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Pop 34.90
Vit 1.90

The Staden Package is a set of interactive tools for DNA sequence assembly and editing, as well as DNA and protein sequence analysis, the best known of which is "gap4".

Download Website Updated 21 May 2014 mcl-edge

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Pop 199.68
Vit 93.68

MCL-edge is an integrated command-line driven workbench for large scale network analysis. It includes programs for the computation of shortest paths, diameter, clustering coefficient, betweenness centrality, and network shuffles. A module for loading and analyzing gene expression data as a network is provided. The MCL algorithm is a fast and highly scalable cluster algorithm for networks based on stochastic flow. The flow process employed by the algorithm is mathematically sound and intrinsically tied to cluster structure, which is revealed as the imprint left by the process. The threaded implementation has handled networks with millions of nodes within hours and is widely used in the fields of bioinformatics, graph clustering, and network analysis.

Download Website Updated 14 Apr 2005 FinchTV

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Pop 32.54
Vit 2.35

FinchTV is a way to easily view and edit your DNA sequencer chromatogram data. It can display an entire trace in a scalable multi-pane view, and will also display quality values (when available). You can edit your base calls and save your data to a new chromatogram file for later use, select and copy sequence for use in other applications, and print your trace out to paper or a file. You also have the ability to search your sequence data using regular expressions or simple base queries, to view raw data from .ab1 files, and to reverse complement your sequence and traces.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.