Sequence - Evolution - Function; Computational Approaches in Comparative Genomics
Sequence - Evolution - Function is an introduction to the computational approaches that play a critical role in the emerging new branch of biology known as functional genomics....2507 days ago
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequenc...in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems...2407 days ago
SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists
This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains...de as well as two binary files. The latter were tested under various operating systems...2397 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence as...ryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s1305...put paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb....2394 days ago
2392 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly...2392 days ago
Mash: fast genome and metagenome distance estimation using MinHash
Mash is normally distributed as a dependency-free binary for Linux or OSX (see https://github.com/marbl/Mash/releases). This source distribution is intended for other operating systems...2378 days ago
3d-dna: 3D de novo assembly (3D DNA) pipeline
This code is designed to enable anyone to reproduce the Hs2-HiC and the AaegL4 genomes r...from Juicer (Durand & Shamim et al., Cell Systems, 2016) and Juicebox (Durand & Robinson et al., Cell Systems...2363 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 s...2288 days ago
repeat-aware: Repeat aware scaffolding evaluation framework by Igor Mandric
Genome scaffolding is a classical challenging problem in bioinformatics. It refers to...e repeats. The previous standard for evaluation (Hunt et al., Genome Biology, 2014) did not take into...2279 days ago