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/read2tree

a tool for inferring species tree from sequencing reads

yuzhenpeng/Workshop

课题组每周研讨会

yuzhenpeng/AKRUP

AKRUP: ancestral karyotype reconstruction universal pipeline

yuzhenpeng/Bioinformatics_notes

Bioinformatics and genomics resources

yuzhenpeng/catfish-genome

Pipelines, code and ressources for creating a fully haplotype-resolved T2T assembly of the African catfish (Clarias gariepinus) combining PacBio HiFi, ONT long reads and Hi-C data.

yuzhenpeng/deduce

鉴定UCE

yuzhenpeng/ERVcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accu

yuzhenpeng/FASSO

FASSO: Functional Annotations using Sequence and Structure Orthology

yuzhenpeng/GAEP

A genome assembly assessment pipeline.

yuzhenpeng/GALBA

GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from a closely related species are available.

yuzhenpeng/GenEra

genEra is an easy-to-use, low-dependency command-line tool that estimates the age of the last common ancestor of protein-coding gene families.

yuzhenpeng/Genome_analysis_scripts

Scripts used for various genomic analyses, including assembly and annotation

yuzhenpeng/haplotype_aware_scaffolding

A series of custom scripts for haplotype aware manual curation of Cannabis genome assemblies

yuzhenpeng/Lab-Code-and-Hacks

This is the site where we store shared code for the Michigan Mycology Lab

yuzhenpeng/locla

LOCLA: Local Optimization for Chromosome-Level Assembly

yuzhenpeng/longevity_project

Workflow for Bat1K longevity project 蝙蝠长寿

yuzhenpeng/Moose_genomics

Moose population genomics

yuzhenpeng/mp-est

MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function

yuzhenpeng/orthology_inference2023

Inference of orthologous proteins in Drosophila genomes

yuzhenpeng/paPAML

new PAML

yuzhenpeng/Phylogeny_tutorial

yuzhenpeng/Plant_Annotation_TEs

Methods and recipes for Plant Genome Annotation - Transposable Elements

yuzhenpeng/Programming_notes

Programming-related notes

yuzhenpeng/quarTeT

A telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat identification

yuzhenpeng/RNA-seq_notes

A continually expanding collection of RNA-seq tools

yuzhenpeng/SHOOT

SHOOT.bio - the phylogenetic search engine

yuzhenpeng/syntplot

Scripts for plotting genome synteny based on BLAST alignment

yuzhenpeng/TRACCER

Convergence analysis using relative rate and correcting for phylogenetic relatedness

yuzhenpeng/VariabilityInTEs

yuzhenpeng/Zoonomia_Cell-TACIT_fine-mapping

Machine learning models of conserved regulatory elements and human genetics of neuropsychiatric traits