Results for "parallel"
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Many-Core Engine (MCE) for Perl example
MCE spawns a pool of workers and therefore does not fork a new process per each element of data. Instead, MCE follows a bank queuing model. Imagine the line being the data and bank-tellers the parallel workers. MCE enhances that model by adding the ability to chunk the next n elements from the in...Tags: Bioinformatics, Programming, Perl, MCE, Parallel, Core, Thread, Fork
2665 days ago
MSAProbs - Parallel and accurate multiple sequence alignment
MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAli...Tags: MSAProbs, Parallel, accurate, multiple, sequence, alignment
1776 days ago
Π-cyc: A Reference-free SNP Discovery Application using Parallel Graph Search
Reference free SNP search for comparative population genomics: multiple samples run simultanously. **experimental phase, compiles and runs with OpenMPI-1.8.8 with Intel Compiler only Cycles enumeration (aka Bubbles) as part of de novo de bruijn graphs assembly using colours can be unpractical fo...Tags: Π-cyc, Reference-free, SNP, Discovery, Application, Parallel, Graph, Search
1573 days ago
PaReBrick: PArallel REarrangements and BReaks identification toolkit
PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the ne...Tags: PaReBrick, Parallel, Rearrangements, Breaks, identification, toolkit
954 days ago
CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLAST) has revolutionized the field of bioinformatics, and is currently i...Tags: CrocoBLAST, Optimized, parallel, local, sequence, alignment, algorithms
2490 days ago
pWhatsHap: a parallel, high-performance version of WhatsHap
Given the potential relevance of efficient haplotyping in several analysis pipelines, we have designed and engineered pWhatsHap, a parallel, high-performance version of WhatsHap. pWhatsHap is embedded in a toolkit developed in Python and supports genomics datasets in standar...Tags: pWhatsHap, parallel, high-performance, WhatsHap, Phasing, Phase, Genome, Alles, Haplotype
2013 days ago
PilonGrid: parallel wrapper around the Pilon framework
The distribution is a parallel wrapper around the Pilon framework The pipeline is composed of bash scripts, an example mapping.fofn which shows how to input your fastq files (you give paths to the R1 file), and how to launch the pipeline.Tags: PilonGrid, parallel, wrapper, Pilon, framework
1984 days ago
VirtualFlow: a versatile, parallel workflow platform for carrying out virtual screening
related tasks on Linux-based computer clusters of any type and size which are managed by a batchsystem (such as SLURM). Currently, there exist two versions of VirtualFlow, which are tailored to different types of tasks: VFLP: VirtualFlow for Ligand Preparation VFVS :&nb...Tags: VirtualFlow, versatile, parallel, workflow, platform, carrying, virtual, screening
1436 days ago
