yuzhenpeng

Al2PrunedTree

Prunes a given newick tree file to keep only taxa present in a given sequence alignment (FASTA format)

bio_tools

Useful bioinformatic scripts

biodiversity_genomics_course

biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute

bioscripts

several scripts for bioinformatics

cactus

Official home of genome aligner based upon notion of Cactus graphs

Centromere_synteny_project

How to identify genome-wide synteny with LASTZ alignment

GenomeAlignmentTools

Tools for improving the sensitivity and specificity of genome alignments

last-genome-alignments

Sequence-manipulation

A range of different perl scripts for manipulating sequences, conducting alignments, consensus sequences, changing formats

yuzhenpeng.github.io

This is my blog files

yuzhenpeng/biodiversity_genomics_course

biodiversity genomics course by Nicol Rueda, Karin Näsvall and Joana Meier from the Wellcome Sanger Institute

yuzhenpeng/HapHiC

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

yuzhenpeng/SynGAP

yuzhenpeng/Vertebrate_Chemoreceptors_mining

Full automatic pipelines to mine OR, TAAR, V2R and V1R genes from any vertebrate genome

yuzhenpeng/2024_phylogenomics_workshop

2024 workshop on phylogenomics, organized by Evomics

yuzhenpeng/BioKIT

a versatile toolkit for processing and analyzing diverse types of sequence data

yuzhenpeng/CAU-T2T-Sheep

A complete telomere-to-telomere assembly of sheep: T2T-sheep1.0

yuzhenpeng/chaintools

Utilities for the genomic chain format

yuzhenpeng/compleasm

基于miniprot评估基因组完整性

yuzhenpeng/CRAQ

基因组组装质量评估和改进的新方法

yuzhenpeng/DupLoss-2

基于基因重复和丢失改进的系统基因组物种树推断

yuzhenpeng/egapx

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

yuzhenpeng/Extract_Consensus_Sequences_of_Genes_from_BAM_parallel

This is a series of scripts on the rapid construction of target interval consensus sequences from bam files and the rapid construction of phylogenetic trees as well as visualisations

yuzhenpeng/Genome_assembly_annotation

Scripts and pipeine for Genome_assembly_annotation

yuzhenpeng/GenomeAnnotation-TOGA

TOGA注释

yuzhenpeng/leviosam2

Fast and accurate coordinate conversion between assemblies

yuzhenpeng/LiftOn

🚀 LiftOn: Accurate annotation mapping for GFF/GTF across assemblies

yuzhenpeng/loco-pipe

低覆盖率全基因组测序的群体基因组学自动化管道

yuzhenpeng/MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies

yuzhenpeng/nwkit

Newick tree processing

yuzhenpeng/OrthoSLC2

OrthoSLC: A pipeline to get Orthologous Genes using Reciprocal Best Blast Hit (RBBH) Single Linkage Clustering, indenpendent of relational database management system

yuzhenpeng/pasta

PASTA (Practical Alignment using SATe and Transitivity)

yuzhenpeng/Phylogenomics1

快速构建高质量系统发生基因组学数据集：脚本使用和指南

yuzhenpeng/Population_genomics_pipline

yuzhenpeng/reciprologs

Find reciprocal best hits (DIAMOND or BLAST) between two (or more!) sets of sequences.

yuzhenpeng/SegDupAnnotation2

Count gene duplications.

yuzhenpeng/T2Tools

T2Tools is a toolset contains several tools for T2T assembly, and it is under development.

yuzhenpeng/taffy

This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files

yuzhenpeng/ToxCodAn-Genome

基因组组装中的基因注释

yuzhenpeng/Vargas-Chavez_et_al_2024_Chromosome_shattering_clitellate_origins

Repository for code and files related to the manuscript Vargas-Chávez et al. 2024. A punctuated burst of massive genomic rearrangements by chromosome shattering and the origin of non-marine annelids