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 A...2225 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 sequencing reads (both DNA...gle reference genome). Based on an extension of BWT for gr...dex (HGFM). more at https://ccb.jhu.edu/software/hi...2204 days ago
EvidentialGene: tr2aacds, mRNA Transcript Assembly Software
EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct hig...h quality, accurate gene sets for animals and plants, developed...gene prediction and assembly software, combining all evidence for genes, from expressed sequenc...2204 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 a...2183 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a DNA...in alignment so that it becomes more suitable for phylogenetic analysis. This s...selected from a protein alignment. Further information can be found in the online docu...2179 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 s...e conduct a commonly used time estimation method, "Approximate Likelihood Method", for the dat...2179 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 RepeatMasker about transp...equences and get some quantitative information. Assemble RepeatMask...ta files Compute summary statistics for ea...E families http://doua.prabi.fr/software/on...2177 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 nov...s name describes the strategy that it implements for genome assembly: PRICE uses paired-read informat...ny other assembler. http://derisilab.ucsf.edu/software/pr...2170 days ago
D-GENIES: A tool for Dotplot large Genomes in an Interactive, Efficient and Simple way
D-GENIES – for Dotplot large Genomes in an Interactive, Efficient and Simple way – is an online tool...2170 days ago
RestrictionDigest: A powerful Perl module for simulating genomic restriction digests
RestrictionDigest can simulate the reference genome digestion and generate comprehensive information of the simulation. It can simulate sing...generates concise comparison of enzyme(s) performan...tion, please see the academic paper published online (htt...2169 days ago