AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGra...2262 days ago
HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads
HISAT2 is a fast and sensitive alignment program for mapping next-generation seque...all indexes (called local indexes), combined with several al...x (HGFM). more at https://ccb.jhu.edu/software/hisat2/index.shtml2241 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Di...ilable best-of-breed gene prediction and assembly software, combining all evidence for g...t aligned (genome-free) locus identification. All software developed for EvidentialGene...2241 days ago
kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity
The k-mer Weighted Inner Product. This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calcula...2220 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is p...2216 days ago
“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files
One code to find them all is a set of perl scripts to extract useful information from Re...working with only a user-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all...2214 days ago
PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++.
We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo geno...rom a prior run of PRICE or any other assembler. http://derisilab.ucsf.edu/software/price/2207 days ago
MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
MECAT is an ultra-fast Mapping, Error Correction and de novo Assembly Tools for single molecula sequencing (SMRT) reads. MECAT employs novel alignment and error correcti...2238 days ago
fragScaff: Genome Assembly with Contiguity Preserving Transposition
Contiguity preserving transposition and sequencing (CPT-seq) is an entirely in vitro mea...ely sequenced long fragments ranging from 5 kilobases to >1 megabase. This software, fragScaff, leverages coincid...2235 days ago
GAPPadder: A Sensitive Approach for Closing Gaps on Draft Genomes with Short Sequence Reads
This software is provided ``as is” without warranty of any kind. In no event shall the author be held responsible for any damage resulting from the use of this software. The program package, includi...2235 days ago