my bin directory

A parallel wrapper for LTR_FINDER

Scripts for bioinformatics data processing and analysis

Practical, reusable scripts for bioinformatics

A box of genomics tools

Phylogenetic and taxonomic analysis for genomes and metagenomes

Script to help assessing the evolutionary history of a TE family

Random perl and shell scripts plus notes for whole genome CDS positive selection detection

Genome Scripts used in fungal comparative genomics

Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish

Scripts and other material for the assembly and analysis of ratite genomes.

RepeatMasker Analysis Pipeline

useful perl scripts and modules

PASA software

Evolutionary Chromosome Breakpoints Validator

A Circos-based tool to visualize genome assembly consistency

VESPA: Very large-scale Evolutionary and Selective Pressure Analyses

整理常用的群体遗传学分析流程和脚本

Create genomic databases with SIFT predictions. Input is an organism's genomic DNA (.fa) file and the gene annotation file (.gtf). Output will be a database that can be used with SIFT4G_Annotator.j…

Genome Scripts used in fungal comparative genomics

Trinity RNA-Seq de novo transcriptome assembly

Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.

(Mostly) Perl scripts that do something related to phylogenomic analysis.

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

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

Discover pseudogenes in a newly assembled genome, using reference gene/protein sequences.

Random perl and shell scripts plus notes for whole genome CDS positive selection detection

This folder contains scripts to access/use the TreeFam database

Source code from Zhang et al., (2014) Genomic data of avian phylogenomics project. GigaScience 3:26

Job management for the Ensembl Genebuild pipeline