Tags: Bioinformatics, Analysis, NGS, GenomeScope, Genome, Stats, Estimate, Heterozygosity, repeat content, Statistical
2355 days ago
FSA: Fast Statistical Alignment
FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FS...Tags: Bioinformatics, FSA, Fast, Statistical, Alignment, DNA, Sequence
2655 days ago
S-plot2: Rapid Visual and Statistical Analysis of Genomic Sequences
S-plot2 creates an interactive, two-dimensional heatmap capturing the similarities and dissimilarities in nucleotide usage between genomic sequences (partial or complete). In S-plot2, whole eukaryotic chromosomes and smaller prokaryotic genomes can be efficiently compared. The tool includes funct...Tags: S-plot2, Rapid, Visual, Statistical, Analysis, Genomic, Sequences
2051 days ago
NanoSim: nanopore sequence read simulator based on statistical characterization.
NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis and gen...Tags: NanoSim, nanopore, sequence, read, simulator, statistical, characterization
2340 days ago
nQuire: a statistical framework for ploidy estimation using next generation sequencing
nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemente...Tags: nQuire, statistical, framework, ploidy, estimation, next, generation, sequencing, NGS
2050 days ago
nQuire: A statistical framework for ploidy estimation using NGS short-read data
nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on...Tags: statistical, framework, ploidy, estimation, NGS, short-read, data
1931 days ago
Tags: Trelliscope, lexibly, visualize, large, complex, data, detail, R, statistical, programming, environment
1576 days ago
Tags: Bio7, integrated, development, environment, ecological, modeling, scientific, image, analysis, statistical, analysis
1558 days ago
Tags: Sequence, Ontology, Bioinformatics, Analysis, SOBA, tool, statistical, graphical, summary, annotated, genome
1393 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
SHAMAN is a shiny application for differential analysis of metagenomic data (16S, 18S, 23S, 28S, ITS and WGS) including bioinformatics treatment of raw reads for targeted metagenomics, statistical analysis and results visualization with a large variety of plots (barplot, boxplot, heatmap, &hellip...Tags: SHAMAN, user-friendly, website, metataxonomic, analysis, raw, reads, statistical, analysis
1367 days ago