Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary b...a about organisms. Its emphasis is on phylogenetic analysis, but some of its modules conc...ics, while others do non-phylogenetic multivariate analysis. Because it is modular, the a...2538 days ago
Mulan: MUltiple sequence Local AligNment and conservation visualization tool
Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full loca...egy that ensures a recapitulation of evolutionary sequence rearrangements (such as inver...ols to align either "draft" or "finished" quality sequence...2536 days ago
CrocoBLAST: Optimized parallel implementation of local sequence alignment algorithms
Local sequence alignment is a cornerstone of bioinformatics, allowing to compare the amino-acid sequences of different proteins, or the nucleotide sequences of different pieces of DNA. The Basic Local Alignment Search Tool (BLA...2531 days ago
Sequence - Evolution - Function; Computational Approaches in Comparative Genomics
Sequence - Evolution - Function is an introduction to the computational approache...ential and limitations of computational and experimental approaches to genome analysis.2519 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to t...More than 95% of the genome is recovered, with no errors; half the assembled sequence...2426 days ago
QuorUM: An Error Corrector for Illumina Reads
Illumina Sequencing data can provide high coverage of a genome by relatively short (most often 100 bp to 150 bp) rea...on in errors due to both changes in individual bases and trimming of unusable sequence...2424 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 sequence...2418 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
...the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxobl...ces. This or similar types of analysis, in combination with manual c...a to public repositories. Our analysis pipeline is open-source and f...2410 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 MinI...2409 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 prediction...which combine these predictions for all sequences to be classified, RITA uses...constitute the highest-confidence set. Sequence...2406 days ago