RSS 175 projects tagged "Bioinformatics"

No download Website Updated 12 Apr 2014 wunderbar

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Pop 17.52
Vit 2.96

Wunderbar is a program which is able to identify mislabeled samples in genotype data when a few extra independent genotypes are available ("genetic barcoding"). Wunderbar calculates the likelihood that genotype mismatches have occurred by chance. It is capable of reliable and sensitive detection of sample mismatches and swaps even in the presence of numerous genotyping errors and in the presence of linkage disequibrilium between the individual genotypes. It only requires a few SNPs to work well.

Download No website Updated 18 Nov 2012 codonPhyML

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Pop 15.36
Vit 22.77

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.

No download No website Updated 25 Sep 2012 Bio::SeqReader

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Pop 21.31
Vit 1.00

Bio::SeqReader provides a lightweight alternative to Bioperl when all you really need is a helper for reading sequence data. The Bio::SeqReader::Fastq class correctly handles FASTQ input with multiline sequence or quality data.

Download Website Updated 29 Sep 2012 Fqutils

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Pop 33.54
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 16 Apr 2014 Orthanc

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Pop 210.98
Vit 52.10

Orthanc is a lightweight, RESTful DICOM server for health care and medical research.

Download No website Updated 26 Oct 2012 VPLG

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Pop 23.07
Vit 2.01

Visualization of Protein Ligand Graphs (VPLG) uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, usually alpha helices and beta strands) or ligand molecules, while the edges model contacts and relative orientations between them. The graphs can be visualized, written to a database, and saved in a text-based file format.

Download Website Updated 28 Jul 2012 MSAProbs

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Pop 17.32
Vit 2.03

MSAProbs is a protein multiple sequence alignment algorithm. It achieves the statistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, and OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons, and Probalign.

Download Website Updated 30 Jul 2012 ScalaBLAST

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Pop 38.26
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 Website Updated 03 Sep 2012 Emergent

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Pop 40.00
Vit 2.74

Emergent is a neural network simulator with a built-in scripting language which allows for the creation and analysis of complex, sophisticated models of the brain in the world. Networks and all of their state variables are visually inspected in 3D, allowing quick "visual regression" of network dynamics and robot behavior. Emergent is a direct descendant of the PDP and PDP++ neural network packages.

No download No website Updated 31 Oct 2011 ODES

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Pop 12.04
Vit 30.05

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.

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Xtables-addons

Additional Netfilter/iptables modules.

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units

A unit converter and calculator.