Mulan: MUltiple sequence Local AligNment and conservation visualization tool
...sions and reshuffling) in any of the species. It combines refine and tba tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic gra...2493 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...2488 days ago
MGRA: Breakpoint graphs and ancestral genome reconstructions
...f ancestor genomes and evolutionary history of extant genomes. It takes as an input a set of genomes represented as sequences of genes (or synteny blocks) and produces such sequences for ancestral genomes at the...2488 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
...mination making the detection of foreign DNA sequences an important part of analysis...the post-assembly detection of contaminating sequences in the published genome of th...ffolds that contain both bacterial and algal sequences. This or similar types of ana...2367 days ago
miniasm: very fast OLC-based de novo assembler for noisy long reads
...e a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate...ey are broadly comparable. Of course, the HGAP3 consensus sequences are much more accurate. In ad...2363 days ago
RITA: Rapid identification of high-confidence taxonomic assignments for metagenomic data
...nlike other hybrid approaches which combine these predictions for all sequences to be classified, RITA uses a...sifier are in agreement, which constitute the highest-confidence set. Sequences not classified in this manner...2363 days ago
Opera: An optimal genome scaffolding program
...6/s13059-016-0951-y.Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Bio...2363 days ago
simNGS and simLibrary – Software for Simulating Next-Gen Sequencing Data
...les, merged clusters, sequence-heterogeneous clusters, etc). Many of these additional sources may optionally applied. simNGS takes fasta format sequences and a file describing the cov...2362 days ago
PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
...the following benefits: PLAST is a high-performance sequence comparison tool designed to compare two sets of sequences (query vs. reference), Reduces the processing time of sequences comparisons while providing h...2359 days ago
MetaSim A Sequencing Simulator for Genomics and Metagenomics.
...s from the metagenome using a simulation of a number of different sequencing technologies. A population sampler optionally produces evolved sequences based on source genomes and a...2356 days ago