RSS 41 projects tagged "Bioinformatics"

Download No website Updated 18 Nov 2012 codonPhyML

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Pop 15.84
Vit 22.88

codonPhyML uses Markovian codon models of evolution in phylogeny reconstruction. Given a set of species characterized by their DNA sequences as input, it will return the phylogenetic tree which best describes their evolutionary relationship.

Download Website Updated 29 Sep 2012 Fqutils

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Pop 33.72
Vit 2.02

Fqutils provides a basic set of bioinformatics command line tools for working with sequence data in FASTQ format. It complements Greg Hannon's fine Fastx Toolkit suite. One characteristic of Fqutils is that it correctly handles the full FASTQ format as described by the published standard, which specifically allows multi-line sequence and quality score information per record. Fqutils is intended to be useful as part of the early portions of post-sequencing pipelines and quality assessment processes.

Download Website Updated 30 Jul 2012 ScalaBLAST

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Pop 37.99
Vit 2.03

ScalaBLAST is a high-performance multiprocessor implementation of the NCBI BLAST library. It supports all 5 primary program types (blastn, blastp, tblastn, tblastx, and blastx) and several output formats (pairwise, tabular, and XML). It will run on most multiprocessor systems which have MPI installed, and can run over a wide variety of interconnects, including infiniband, quadrics, and ethernet. It is designed to run a large number of queries against either large or small databases. It parallelizes the BLAST calculations by dynamically scheduling them across processors using a fault-resilient scheme.

No download No website Updated 31 Oct 2011 ODES

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Pop 11.96
Vit 30.13

ODES is a pthreads parallelized exact algorithm to enumerate all maximal sub-graphs of a graph that exceed a specified cutoff density of at least 1/2, even if they overlap.

Download Website Updated 14 Apr 2011 Scalable Assembler at Notre Dame

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Pop 22.32
Vit 1.04

The Scalable Assembler at Notre Dame (SAND) replaces the early stages of the Celera Assembler with scalable versions that can run on collections of commodity computers. By harnessing clusters, clouds, grids, or just random machines in your office, many bioinformatics tasks can be reduced from weeks or months down to minutes or hours.

Download Website Updated 14 Jul 2009 mkESA

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Pop 32.43
Vit 1.75

mkESA is a program for constructing enhanced suffix arrays (ESAs) from biological sequence data. The program is based on an implementation of Manzini's lightweight Deep-Shallow algorithm, which can also utilize multiple CPUs/cores for extra performance. The generated output is compatible with the output of mkvtree from the Vmatch package.

Download Website Updated 09 Jul 2009 libfid

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Pop 26.50
Vit 1.43

The Full-text Index Data structure library, libfid for short, is a portable software library for accessing indexed data through a simple C interface. It implements, among others, functions for reading indexed data from files, and for performing common operations such as fast string matching. Easy alphabet handling for mapping between printable and binary alphabets is integrated from the ground up. Currently, the enhanced suffix array is the only full-text index data structure supported. A very simplistic program for constructing enhanced suffix arrays is included.

Download No website Updated 13 Feb 2012 Mychem

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Pop 17.38
Vit 3.31

Mychem is an extension that provides a set of functions that permit you to handle chemical data within a MySQL database.

No download Website Updated 07 Mar 2007 xpress-analyzer

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Pop 18.22
Vit 51.05

xpress-analyzer is a suite of programs for analyzing functional genomics data. Programs are included for analysis of variance, multiple test correction for significance tests, a non- linear least square fitting algorithm (four parameters), general linear models, Kolmogorov-Smirnov distance, nearest neighbor algorithm, principal component analysis, and Student's t-test. It is intended to be used as a faster alternative to R on large data sets.

No download Website Updated 24 Feb 2007 PDB2PQR

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Pop 13.38
Vit 51.15

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include adding a limited number of missing heavy atoms to biomolecular structures, determining side-chain pKas, placing missing hydrogens, optimizing the protein for favorable hydrogen bonding, assigning charge and radius parameters from a variety of force fields.

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