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 an...2480 days ago
LIBSVM -- A Library for Support Vector Machines
LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It su...2465 days ago
QuorUM: An Error Corrector for Illumina Reads
...es and trimming of unusable sequence. We developed an error correction software called QuorUM. QuorUM is main...erence assembly is available. QuorUM is distributed as an independent software package and as a module of th...2367 days ago
Unicycler: Hybrid assembly pipeline for bacterial genomes
Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly...2365 days ago
2361 days ago
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication
...tion of new tools in the future. Availability and Implementation The software is implemented in Python 3 an...re/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line vers...2361 days ago
CHSMiner: a GUI tool to identify chromosomal homologous segments
...d cause the degeneration of CHSs. Results Here we present a Java software CHSMiner that detects CHSs ba...terface allows interactive visualization of the results. We tested the software on both simulated and biologi...2357 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...unt how many contigs: grep ">" reads.fa | wc -l # Download sample PacBio from the PBcR website wget -O- http://www.cbcb.umd.edu/software/PBcR/data/selfSampleData.tar....2348 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
RITA is a standalone software package and Web server for taxonomic assignment of metagenomic sequence reads. By combining homology predictions from BLAST or UBLAST with compositio...2348 days ago
DRAWID: user-friendly Java software for chromosome measurements and idiogram drawing
"DRAWID has number of advantages including a user-friendly interactive interface, possibility for simultaneous chromosome and FISH/GISH/banding signal measurement and id...2348 days ago