ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standa...duplications, and (iv) providing seamless integration with the NCBI taxonomy database....2326 days ago
Genome assembly stats plotting
...most commonly used assembly metrics in a single visualisation. Each of these presentations is generated using javascript from a common (JSON) data structure, allowing toggling between al...2317 days ago
2315 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), and...908 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS, an application that utilizes the barcoding information contained in linked reads...ix-fold, using moderate coverage (25-fold) Chromium data. We expect ARCS to have broad...the barcoding information contained in linked read data for...2310 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 abou...2304 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 huge protein sequence se...seqs2 enables sensitive protein sequence searching for the analysis of massive data sets...2294 days ago
2279 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 graphs with JavaScript....network graphs from R. The main idea is that you should able to take an R data fram...2279 days ago
GMOL: An Interactive Tool for 3D Genome Structure Visualization
GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve corresponding genome sequences.2295 days ago