Search Results for "linux shell android" - Page 3

This is an approach that complements previous methods for reliable homozygous structural variation identification. Our approach accurately determines genotype and breakpoints relative to a reference genome based on de novo assembly of Illumina Genome Analyzer sequencing data. In this method, we examined only homozygous structural variations because detecting heterozygous structural variations requires assembly of haplotype sequences, which is not yet possible using existing assemblers.

FFP (Feature frequency profile) is an alignment free comparison tool for phylogenetic analysis and text comparison. It can be applied to nucleotide sequences, complete genomes, proteomes and even used for text comparison.

ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

SIPeS - Site Identification from Paired-end Sequencing

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.

An SQL handler to interface multiple databases data to the OpeNDAP Hyrax (BES) server. Written in C++, it uses unixODBC to query DB and can be dynamically extended to use proprietary ODBC API driver in many easy ways. It is bundled with scripts to ge

cifget is a DDLm dictionary import expansion utility, which generates expanded dictionaries that could be used when reading, writing, or validating CIF files

BCAR is a library for the associative classification, which denotes "Boosting Class Association Rules". BCAR provides a general tool for classification tasks with various types of input data.

This project implements an algorithm for segmenting protein sequences into smaller meaningful blocks. The method is based on the pure statistical approach and it uses an analogy between proteins and natural language.

ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.

The High Throughput Sequence Analysis Pipeline uses freely available bioinformatics tools from NCBI, Phylip, EMBOSS and clustalw to identify and group closely related DNA samples. It can be run on *Nix systems linearly or in parallel using the SGE.

Shell tools for Newick-fromatted trees

The WISDOM project is a Grid based production environment used to deploy bio-informatics large scale applications.

A Folding@Home integrated monitoring environment, designed for Linux, *nix systems and Windows, which is intended to be easy-to-use and provide a flexible, customiseable and "user-friendly" environment for reviewing the status of active F@H clients.

PepArML: An unsupervised, model-free, combining peptide identification arbiter for tandem mass spectra via machine learning.

Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.

Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees.

PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.

ArrayOligoSelector (AOS) systematically designs gene specific long oligo probes for entire genomes. The program optimizes the oligo selections for several parameters, including uniqueness in the genome, internal repeats, self-binding, and GC content.

HomGL is a web-based tool for comparing gene lists obtained e.g. by microarray studies. Unigene, Locus Link & Homology databases are used to compare gene lists with different accession numbers and between different organisms.

(OBSOLETE) trace_utils is a program for processing sequencing trace data. The main goal of this program is to provide a completely free software in detecting SNPs like what polyphred has done, but with even higher accuracy and more flexibility.

'torungmx' is a script to help you running Gromacs

trimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment. These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided, the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment. trimAl implements a series of...

The Integrative Biology VRE is a web-based graphical user interface and repository that provides an environment where biological simulation experiments can be constructed without the need for any knowledge of unix, cluster computing, or shell scripting.