Category Archives: Bioinformatics

GENtle

GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and more. Find GENtle at: http://gentle.magnusmanske.de

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Genomorama

Genomorama is a software program for interactively displaying multiple genomes. It provides a powerful yet easy to use interface that leverages the visualization power of modern computers (via OpenGL) and the substantial bioinformatic infrastructure provided by the NCBI (via the … Continue reading

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DeltaStat

DeltaStat performs statistical calculations on data from 2D gel experiments. DeltaStat combines the power of R, a language for statistics, with the efficiency of a relational database to handle the large amount of data generated in proteomics experiments. Find DeltaStat … Continue reading

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Jalview

Jalview is a multiple alignment editor written entirely in java. Find Jalview at: http://www.ebi.ac.uk/~michele/jalview/

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Readseq

Read & reformat biosequences Find Readseq at: http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

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AnnHyb

AnnHyb is a tool for working with and managing nucleotide sequences in multiple formats. The features includes format conversion, sequence viewer, sequence editor, oligonucleotides alignment, restriction analysis, pattern searching, retrieval from servers, multi-alignment viewer, consensus determination… Find AnnHyb at: http://bioinformatics.org/annhyb/

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The Alkahest Initiative

Alkahest is an initiative to produce free open source software systems for high-throughput DNA sequence data management and analysis. The goal is to produce a comprehensive package for data management and bioinformatics research which is composed of separable but interoperable … Continue reading

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ALiBio: Algorithms Library for Bioinformatics

The goal of ALiBio is the give libraries and efficient fundamental algorithm to be used when developing applications in the bioinformatics field. Find ALiBio: Algorithms Library for Bioinformatics at: http://bioinformatics.org/ALiBio/

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ABE

ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve. Find ABE at: http://bioinformatics.org/abe/

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JAligner – Java implementation of biological sequence alignment algorithms

JAligner is a Java implementation of biological sequence alignment algorithms. Presently, the package implements the pair wise alignment algorithm Smith-Waterman. The basic Dynamic Programming Smith-Waterman algorithm has been modified to support affine (open and extend) gap penalty. Also, Gotoh’s improvement … Continue reading

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