Mulan: MUltiple sequence Local AligNment and conservation visualization tool
Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid...that ensures a recapitulation of evolutionary sequence rearrangements (such as inver...to align either "draft" or "finished" quality sequences. Mulan provides a dynamic gr...2509 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....2504 days ago
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 function...2492 days ago
Meraculous: De Novo Genome Assembly with Short Paired-End Reads
...the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101...2399 days ago
QuorUM: An Error Corrector for Illumina Reads
...we use the term “error correction” to denote the reduction in errors due to both changes in individual bases and trimming of unusable sequence. We developed an error correc...2398 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 databases. DFAST was originally started as an on-line annotation s...2392 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
...amination making the detection of foreign DNA sequences an important part of analysi...the post-assembly detection of contaminating sequences in the published genome of t...based on multiple blastn searches with short sequence fragments. They revealed a nu...2383 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
...erver for taxonomic assignment of metagenomic sequence reads. By combining homology...aches which combine these predictions for all sequences to be classified, RITA uses...which constitute the highest-confidence set. Sequences not classified in this manne...2379 days ago
Opera: An optimal genome scaffolding program
Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information fr...ptimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Bi...2379 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
...se that may be present in real data ("dust", bubbles, merged clusters, sequence-heterogeneous clusters, etc)....additional sources may optionally applied. simNGS takes fasta format sequences and a file describing the co...2378 days ago