Tags: Pango, Lineage, Analysis, Output, Classification, SARS-CoV2
918 days ago
Tags: GO, Analysis, Enrichments
468 days ago
Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
Bactopia is a flexible pipeline for complete analysis of bacterial genomes. The goal of Bactopia is to process your data with a broad set of tools, so that you can get to the fun part of analyses quicker! Bactopia can be split into two main parts: Bactopia Analysis Pipeline, and Bactop...Tags: Bactopia, Flexible, Pipeline, Complete, Analysis, Bacterial, Genomes
5 days ago
PhyloHerb: Phylogenomic Analysis Pipeline for Herbarium Specimens
What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene a...Tags: Phylogenomic, Analysis, Pipeline, Herbarium, Specimens
89 days ago
Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analys...Tags: Mesquite, modular, system, evolutionary, analysis
2498 days ago
poRe: an R package for the visualization and analysis of nanopore sequencing data
Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a s...Tags: poRe, R, package, visualization, analysis, nanopore, sequencing, data
2370 days ago
Scripts for the analysis of HGT in genome sequence data.
Scripts for the analysis of HGT in genome sequence dataTags: scripts, analysis, HGT, genome, sequence, data
2364 days ago
Tags: kSNP3.0, SNP, detection, phylogenetic, analysis, genomes, alignment, reference, genome
2355 days ago
Delta: a new Web-based 3D genome visualization and analysis platform
Delta is an integrative visualization and analysis platform to facilitate visually annotating and exploring the 3D physical architecture of genomes. Delta takes Hi-C or ChIA-PET contact matrix as input and predicts the topologically associating domains and chromatin loops in the ge...Tags: Delta, Web-based, 3D, genome, visualization, analysis, platform
2343 days ago
GIGGLE: a search engine for large-scale integrated genome analysis
GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existi...Tags: GIGGLE, search, engine, large-scale, integrated, genome, analysis
2323 days ago