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/pairLiftOver

Convert genomic coordinates of contact pairs from one assembly to another.

yuzhenpeng/SIFT4G_Create_Genomic_DB

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.jar to annotate VCF files.

yuzhenpeng/Agora

Algorithm For Gene Order Reconstruction in Ancestors

yuzhenpeng/applied-computational-genomics

Applied Computational Genomics Course at UU: Spring 2020

yuzhenpeng/bedmaker

pipeline to convert bigWig, bedGraph and other file types into BED format

yuzhenpeng/bioinfo_tools

TEs analysis

yuzhenpeng/BioPipelines

Pipelines used in bioinfomatic data processing or analysis

yuzhenpeng/CHM13

The complete sequence of a human genome

yuzhenpeng/chromsyn

Chromosome-level synteny plotting using orthologous regions可视化

yuzhenpeng/Comparative-Annotation-Toolkit

yuzhenpeng/Convergent-evolution-of-viviparity-in-Cyprinodontiformes

由卵生到胎生进化

yuzhenpeng/esga2

yuzhenpeng/FalseGeneLoss

Data and scripts for an unpublished paper about false chromosome and gene losses in assemblies caused by sequence and assembly errors

yuzhenpeng/GenErode

研究濒危和灭绝物种有害突变的简易流程

yuzhenpeng/GenomeSyn-1

基因组共线性与结构变异可视化

yuzhenpeng/GenomicBreaks

Pairwise Alignment Breakpoint Analysis

yuzhenpeng/NGenomeSyn

Any Way to Show Multi genomic Synteny

yuzhenpeng/phyloConverge

Characterizing associations between genetic elements with convergent phenotypes.

yuzhenpeng/physalia_adaptation_course

population genomics

yuzhenpeng/pipelines-1

genome assembly pipeline for VGP

yuzhenpeng/poseidon

PoSeiDon: positive selection detection and recombination analysis pipeline

yuzhenpeng/PsiCLASS

多个转录组样本组装

yuzhenpeng/rbh

Finds reciprocal-best-hit matches between two all-by-all BLAST searches

yuzhenpeng/RectChr

Multi-level visualization of genomic statistical variables on rectangular chromosomes

yuzhenpeng/SALSA

SALSA: A tool to scaffold long read assemblies with Hi-C data

yuzhenpeng/SELDLA-G

yuzhenpeng/Synteny-and-rearrangement-of-3-Eucalyptus

Alignment and analysis scripts for "Long-read genome assemblies uncover extensive loss of micro-syntenty and conservation of macro-synteny among three woodland Eucalyptus species."

yuzhenpeng/TDGP

my 3D genome pipeline and scripts repository

yuzhenpeng/TransposonUltimate

TransposonUltimate - a holistic set of tools for transposon identification

yuzhenpeng/Zoonomia_TEs

Scripts and pipelines associated with the submitted publication: "biorxiv-link"