ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providi...uplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely availabl...2331 days ago
Genome assembly stats plotting
A de novo genome assembly can be summarised b y a number of metrics, including...ach of these presentations is generated using javascript from a common (JSON) data structure, allowing toggling...2322 days ago
2320 days ago
PLAR: Pipeline for lncRNA annotation from RNA-seq data
Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), an...913 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS, an application that utilizes the barcoding information c...x-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad...the barcoding information contained in linked read data for connecting high-quality s...2315 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...2309 days ago
MMseqs2.0: ultra fast and sensitive protein search and clustering suite
MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster...eqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, d...2300 days ago
2285 days ago
d3Network:Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.
Mike Bostock’s D3.js is great for creating interactive network graph...etwork graphs from R. The main idea is that you should able to take an R data frame with information about...2285 days ago
ALPHA: A Toolkit for Automated Local Phylogenomic Analyses
Automated Local Phylogenomic Analyses, or ALPHA, is a python-based application that provides an intuitive user interface for phylogenetic analyses and data visualization. It has four di...2300 days ago