Trinity RNA-Seq de novo transcriptome assembly

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

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

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

Any Way to Show Multi genomic Synteny

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

🌳 Create a tree using Mash distances

GET_HOMOLOGUES: a versatile software package for pan-genome analysis

source code for EVM

整理常用的群体遗传学分析流程和脚本

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

A tiny tool for checking the working domain of sci-hub

Practical, reusable scripts for bioinformatics

FEELnc : FlExible Extraction of LncRNA

Few scripts facilitating the extraction of info from Repeat Masker .out files

Genome annotation pipeline

Allele-specific alignment sorting

Tool set for processing fasta/fastq/table formated data. Usually they are perl scripts.

BITACORA: A Bioinformatics tool for gene family annotation

The SYNY pipeline investigates synteny between species by reconstructing protein clusters from gene pairs.

Multi-level visualization of genomic statistical variables on rectangular chromosomes

TD2

A pipeline for genomic variant detection with genome assemblies at population scale

scripts to parse and analyse MCScanX collinearity output

Diamond2GO is a set of tools that can rapidly assign Gene Ontology (GO) terms and perform functional enrichment for large-scale functional genomics datasets.

fusion transcript detection using long reads, leveraging ctat-minimap2 and FusionInspector