228 projects tagged "Bioinformatics"

No download No website Updated 15 May 2014 QtIPy

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Pop 23.15
Vit 3.65

QtIPy is a simple GUI-based automator for IPython notebooks. It allows you to attach triggers to files, folders, or timers to automatically run notebooks. IPython notebooks are great for interactively working through analysis problems, so why would you want to automatically run them? To get a record of how you ran your analysis! By running a notebook through QtIPy you get the output, figures, and a step by step log of how the analysis was performed all in the same folder.

No download Website Updated 12 Apr 2014 wunderbar

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Pop 36.10
Vit 6.84

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 30 Apr 2014 Pathomx

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Pop 145.30
Vit 11.73

Pathomx is a workflow-based tool for the analysis of metabolomic and other omics datasets. It is interactive, visual, extensible, intelligent, and free for any use. It lets you dynamically build analysis workflows using the interactive editor. Drag and drop connections between plugin tools to create a complete workflow through which to run your analysis. Data can be loaded and processed automatically, and new approaches tested simply by connecting tools.

Download No website Updated 18 Nov 2012 codonPhyML

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Pop 16.25
Vit 23.59

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 20.98
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 33.36
Vit 2.01

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 25 May 2014 SimThyr

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Pop 59.63
Vit 42.36

SimThyr is a continuous simulation program for pituitary-thyroid feedback control. Applications of this program cover research, including development of hypotheses, and education of students in biology and medicine, nurses, and patients.

Download Website Updated 08 May 2014 Orthanc

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Pop 179.09
Vit 24.27

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 21.93
Vit 1.99

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 17.61
Vit 2.01

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.

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Open Camera

A camera app for Android.

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mcl-edge

A command-line network analysis workbench.