Trinity RNA-Seq de novo transcriptome assembly

Automatically exported from code.google.com/p/cdhit

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Another Gtf/Gff Analysis Toolkit

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

Extensive de-novo TE Annotator

TransDecoder source

A minimap2 frontend for PacBio native data formats

Any Way to Show Multi genomic Synteny

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data

Application of pan-genome for population

Multi-level visualization of genomic statistical variables on rectangular chromosomes

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniP…

Genome annotation pipeline

Bulked-Segregant Analysis using vcf file with or without parents

Various bioinformatics tools

The scripts used in the project "The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in Arabidopsis thaliana"

LD-based phasing algorithm for segregating F1 populations (pseudo-oneway testcross)