RSS 99 projects tagged "Bioinformatics"

No download Website Updated 22 Mar 2010 Ascalaph

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Pop 22.07
Vit 38.57

Ascalaph is a general purpose 3D graphical molecular modeling suite that performs molecular mechanics and molecular dynamics simulations as well as quantum mechanics calculations.

Download Website Updated 14 Jul 2009 mkESA

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Pop 32.25
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 17 Jun 2008 IU Parallel FastDNAML

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Pop 8.00
Vit 46.13

IU parallel fastDNAml is a program that infers evolutionary histories from genetic sequences, modified and extended from the serial version of fastDNAml to run in parallel on heterogeneous and widely distributed systems.

Download No website Updated 13 Feb 2012 Mychem

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Pop 17.66
Vit 3.32

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

Download Website Updated 19 Nov 2008 Java Machine Learning Library

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Pop 39.51
Vit 1.91

The Java Machine Learning Library is a set of reference implementations of machine learning algorithms. These algorithms are well documented, both in the source code as on the documentation site. Along with real machine learning algorithms, many supporting algorithms are provided: distance measures, evaluation criteria, data sets for validation purposes, and some sample code.

Download Website Updated 14 Feb 2008 SNPfile

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Pop 17.41
Vit 1.82

SNPfile is a library and API for manipulating large SNP data sets with associated meta-data, such as marker names, marker locations, individuals' phenotypes, etc. in an I/O efficient binary file format. In its core, SNPfile assumes very little about the metadata associated with markers and individuals, but leaves this up to application program protocols.

Download Website Updated 26 Dec 2012 massXpert mass spectrometry package

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Pop 213.12
Vit 16.63

The massXpert software package is a mass spectrometry environment for linear (bio-)polymers. It inherits all the innovations of GNU polyxmass. It allows the detailed definition of new polymer chemistries in the XpertDef module. These chemistry definitions are then used in the desktop calculator-like mass calculator (XpertCalc) and in the sophisticated polymer sequence editor and (bio-)chemical/mass spectrometric simulations module (XpertEdit). Available simulations include polymer and monomer chemical modifications, polymer sequence cleavage, gas-phase fragmentation, m/z ratio calculations, and more.

No download Website Updated 24 Feb 2007 PDB2PQR

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Pop 13.15
Vit 51.07

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.

No download Website Updated 24 Feb 2007 APBS

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Pop 23.62
Vit 51.07

APBS is a software package for the numerical solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum electrostatics plays an important role in several areas of biomolecular simulation, including simulation of diffusional processes to determine ligand-protein and protein-protein binding kinetics, implicit solvent molecular dynamics of biomolecules, solvation and binding energy calculations to determine ligand-protein and protein-protein equilibrium binding constants and aid in rational drug design, and biomolecular titration studies.

Download Website Updated 04 May 2007 PrIMETV

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Pop 15.30
Vit 1.80

PrIMETV is a program that can visualize tree-within-tree phenomena such as gene/species tree reconciliations. Output can be given in a range of formats, including PostScript, Fig, and SVG. Thus, it is possible to easily edit the final illustration in many available drawing programs. PrIMETV can also directly manipulate important attributes such as color and layout policy.

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Tonido

Access, share, and sync from anywhere and any device.

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QCAD

A 2D CAD program.