Search Results for "learning linux command line" - Page 5
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Showing 171 open source projects for "learning linux command line"
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BLOSpectrum tools provide programs to automatically classify proteins according to SCOP database. In order to achieve such a goal, they implements all the required information theory widgets on BLOSpectrum fingerprints.
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BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.
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YaSeTo implements a modification of the widely used Sankoff-Algorithm for sequence/structure alignments of RNA sequences. It is suitable for genome-wide ncRNA gene finding, in case the ncRNA exhibits a conserved secondary structure.
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Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.
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Common code developed by researchers in the Edwards Bioinformatics Group at SDSU. This code is free for everyone to use. It is our base code that we provide on an as-is basis. Please let us know if you use the code or have questions/comments
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The BioSimz project aims to deliver a library (as well as the interface) to conduct large-scale biomolecular simulations at their atomic scales of detail. The initiative idea is to observe the protein crowding in vivo; it now can do much more than that!
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qips is a software package for analyzing ChIP-seq ("Chromatin ImmunoPrecipitation on sequencing") data. It finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase.
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Given low-density genotypes for pedigrees, and dense genotypes for some people in those pedigrees, computes high-density genotypes for some other people in those pedigrees. This reduces genotyping effort.
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The SBML ODE Solver is a command-line tool and programming library (ISO/ANSI C) for construction and numerical integration of an ODE system, derived from an SBML based description of a biochemical reaction network. Development has moved to https://github.com/raim/SBML_odeSolver . Please download the latest version from there!
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EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
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Whole-genome scale multiple genome local alignment search program. Supports unlimited length gapped-seed patterns, parallelization through distributed hashing, and unique a TF-IDF based repeat filtering method.
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Stand-alone software tool for the interactive CE analysis of microarray data. The software is a user-friendly and allows on-the-fly study of CE
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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
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LocalMotif is a bioinformatics tool for discovering nucleotide motifs in a set of gene regulatory sequences. It takes into account the positional distribution of the motifs relative to a biological landmark. Look out for an updated version in May.
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The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size.
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slclust: a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. The slclust utility is written in ANSI C++.
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PTools : a C++/Python library for macromolecular docking
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Fast5 is a probabilistic file format for the storage of nucleotide and protein sequences based on hdf5.
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MUMmerGPU is a high-throughput DNA sequence alignment program that runs on nVidia G80-class GPUs. It aligns sequences in parallel on the video card to accelerate the widely used serial CPU program MUMmer.
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Software to cluster protein sequences into functionally similar groups. Journal reference: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/16/1765
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dprimer is a command line utility for designing degenerate PCR primers against multiple, aligned sequences. Its primary use case is searching for a family of related pathogens in a host tissue sample.
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