Dot, an interactive viewer for genome-genome comparison
Dot, an interactive dot plot viewer that allows genome scientists to visualize genome-ge...ments in order to evaluate new assemblies and perform exploratory comparative genomics. Dot supports the outp...2345 days ago
PGAP-X: Extension on pan-genome analysis pipeline
PGAP-X is a microbial comparative genomic analysis platform with graphic interface. Seri...and methodologies have been developed and integrated to analyze and visualize genomics structure variation, gene dis...2336 days ago
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new...2309 days ago
Mesquite: A modular system for evolutionary analysis
Mesquite is modular, extendible software for evolutionary biology, designed to help biologists organize and analyze co...ms. Its emphasis is on phylogenetic analysis, but some of its modules concern populati...2287 days ago
EWAS: epigenome-wide association study software 2.0
EWAS2.0 can analyze EWAS data and identify the association between epigenetic variations and disease/phenotype. On the...more distinctive features. EWAS2.0 software was developed based on our “populati...2279 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-gener...ncing reads (both DNA and RNA) to a population of human genomes (as well as...global GFM index that represents a population of human genomes, HISAT2 uses...0 indexes needed to cover the human populati...2231 days ago
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HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence r...ncing (Fosmid or BAC clones) SMRT reads (PacBio) Oxford Nanopore reads 10X Genomics Linked-Reads proximity-ligat...2224 days ago
SALSA: A tool to scaffold long read assemblies with Hi-C
This code is used to scaffold your assemblies using Hi-C data. This version implements s...Scaffolding of long read assemblies using long range contact information. BMC genomics, 18(1), 527. Link Ghurye,...2193 days ago
ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly
With increased availability of de novo assembly algorithms, it is feasible to study enti...ient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics 18(Suppl 4):387.2175 days ago