Search Results for "sql command line" - Page 25
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Showing 635 open source projects for "sql command line"
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LineageEvolver is a simulation system for molecular evolution. Sequence evolution is simulated using modular processes such as substitutions, gene duplication/death, horizontal gene transfer, and more.
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neochip is a collection of algorithms for high-density oligonucleotide microarrays. The current version contains heuristic algorithms that attempt to improve the quality of arrays by re-designing their layout (the location of the probes on the chip).
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runsbml - Pathway Simulation Tool emulates the dynamics of biological pathways by calculating concentrations of biochemical compounds at different times and conditions.
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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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The phase machine program allows supervised classification of DNA sequence data from different populations using haplotype sequences generated by the PHASE program.
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Multilayered feed-forward neural network software written in C++. Backpropagation and RPROP are available as training algorithms. Design goals: speed of execution when calculating the output to new data, and quality of training (preprocessing: PCA).
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A command-line program to manipulate annotated genetic sequences (initially in EMBL format). The user supplies a pattern to identify which features or qualifiers to process. These can then be deleted, renamed etc
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Phight - a phylogeny tree building program Currently, it supports Likelihood method and distance method. This program will includes diagnostic function as a special feature.
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Yawn: Yet Another W* Network: a java framework for developing, training and testing neural networks independently of the model and test environment.
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lazar (Lazy Structure-Activity Relationships) is a tool for the prediction of toxic activities of chemical structures.
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For interactive clustering and visualization, Cluster and TreeView by Mike Eisen are great. XCluster by Gavin Sherlock solves the problem of clustering large numbers of files. Now slcview allows you to script generation of cluster and tree images.
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NeoBio is a Java class library of Computational Biology Algorithms. The current version consists mainly of pairwise sequence alignment algorithms such as the classical dynamic programming methods of Needleman-Wunsch and Smith-Waterman.
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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.
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gbwget is a command line/screen oriented tool to search in nucleotide or protein databases and to view or retrieve database entries. It can easily integrated into the EMBOSS seqence analysis Suite can also be used standalone.
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Parallel version of MUMMER v. 3.14, a genome-level alignment tool used to assemble complete genomes.
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malty_DEPRECATED
translates alignments of A-to-B and B-to-C to A-to-C; has BAM support
Development moved to: https://bitbucket.org/rongchenlab/malty Docs moved to: http://malty.readthedocs.org/en/latest/ -
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A software framework to support distributed evolutionary software development. It dynamically creates a network of nodes that can run a pre-distributed source code (e.g. artificial lifeforms). The results of the calculation will be sent back to the maste
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This collection of tools written in C++ with the STL library provides the basic building blocks to develop complex analysis pipelines on genomic coordinates.
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AQUA is a suite of programs for Analyzing the QUAlity of biomolecular structures that were determined via NMR spectroscopy. AQUA was developed by Ton Rullmann and Jurgen Doreleijers in the NMR Spectroscopy Department, Utrecht.
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The program fuses 2 sets of molecules. It tries different relative positions of molecules before binding them, so that there is no or minimal intersection in the resulting molecule. The atom to be fused in a molecule is labeled with an R symbol.
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Paired Sequence File Comparison
Fast validation of FASTQ files containing paired-end reads
For a summary and user's guide, please see the Wiki page: https://sourceforge.net/p/psfc/wiki/Home/ The Wiki page can also be accessed via the top toolbar.
