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/20385726Tags: 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
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
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
Tags: Heap, sensitive, accurate, SNP, detection, tool, low-coverage, high-throughput, sequencing, data
2171 days ago