Results for "Detection"

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  • DeCoSTAR - Detection of Co-evolution

    DeCoSTAR is a software which aims at reconstructing ancestral gene or genome organizations, in the form of sets of neighborhood relations -adjacencies- between pairs of ancestral genes or gene domains.Ancestral genes or domains are deduced from reconciled gene trees in a context of birth, speciat...

    Tags: Bioinformatics, DeCoSTAR, Detection, Co-evolution, Reconstruction, Ancestral, Gene, Genome

    2541 days ago

  • NovelSeq: Novel Sequence Insertion Detection

    The NovelSeq framework is designed to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. http://novelseq.sourceforge.net/Home Paper at https://www.ncbi.nlm.nih.gov/pubmed/20385726

    Tags: NovelSeq, Novel, Sequence, Insertion, Detection

    2485 days ago

  • alienness : Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

    Horizontal gene transfer (HGT) is the transmission of genes between organisms by other means than parental to offspring inheritance. While it is prevalent in prokaryotes, HGT is less frequent in eukaryotes and particularly in Metazoa. Here, we propose Alienness, a taxonomy-aware web application a...

    Tags: alienness, Rapid, Detection, Candidate, Horizontal, Gene, Transfers, Tree, Life

    2209 days ago

  • ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

    ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from the data). By "cohort" we mean samples sequenced ...

    Tags: ClinCNV, Detection, copy, number, changes, Germline, Trio, Somatic, NGS, data

    1533 days ago

  • MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriants

    MALVA is able to genotype multi-allelic SNPs and indels without mapping reads MALVA calls correctly more indels than the most widely adopted genotyping pipelines Mapping-free approaches are as accurate as alignment-based ones, while being faster More at https://www.sciencedirect.com/scien...

    Tags: MALVA, Genotyping, Mapping-free, ALlele, Detection, Known, VAriants, snp

    1522 days ago

  • MimiLook: A Phylogenetic Workflow for Detection of Gene Acquisition in Major Orthologous Groups of Megavirales

    This tool detects statistically validated events of gene acquisitions with the help of the T-REX algorithm by comparing individual gene tree with NCBI species tree. In between the steps, the workflow decides about handling paralogs, filtering outputs, identifying Megavirale specific OGs, detectio...

    Tags: MimiLook, Phylogenetic, Workflow, Detection, Gene, Acquisition, Major, Orthologous, Groups, Megavirales

    809 days ago

  • Harvest: a suite of core-genome alignment and visualization tools

    Harvest is a suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes, including variant calls, recombination detection, and phylogenetic trees. Tools Parsnp - Core-genome alignment and analysis Gingr - Interactive ...

    Tags: Harvest, alignment, visualization, intraspecific, microbial, genomes, recombination, detection, phylogenetic, trees

    2303 days ago

  • kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome

    Sept. 20, 2017 Version 3.1 released. Major upgrade. Version 3.1 fixes the problems with SNP annotation that arose when NCBI discontinued use of GI numbers. Please read carefully the Preface (page 3) and the File of annotated genomes section (pages 9-10) in the version 3.1 User Guide. Thanks to To...

    Tags: kSNP3.0, SNP, detection, phylogenetic, analysis, genomes, alignment, reference, genome

    2303 days ago

  • Computational resources for TE discovery and TE detection

    Transposable Elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Following are the list of resource and location for TE dis...

    Tags: Computational, resources, TE, discovery, detection, Transposable, Elements (TEs)

    2237 days ago

  • Heap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput sequencing data

    Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls SNPs at each site except for sites at the both end ...

    Tags: Heap, sensitive, accurate, SNP, detection, tool, low-coverage, high-throughput, sequencing, data

    2171 days ago