zhenpeng yu's repositories
Vertebrate_Chemoreceptors_mining
Full automatic pipelines to mine OR, TAAR, V2R and V1R genes from any vertebrate genome
AKRUP
AKRUP: ancestral karyotype reconstruction universal pipeline
bioinformatics-perl-scripts
Useful scripts for various things
BioSAK
A Swiss-Army-Knife for Bioinformaticians
CAGEE
Computational Analysis of Gene Expression Evolution
chaintools
Utilities for the genomic chain format
ClipKIT
a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference
compleasm
基于miniprot评估基因组完整性
CRAQ
基因组组装质量评估和改进的新方法
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
GAEP
A genome assembly assessment pipeline.
Genome_analysis_scripts
Scripts used for various genomic analyses, including assembly and annotation
Genome_assembly_annotation
Scripts and pipeine for Genome_assembly_annotation
GenomeAnnotation-TOGA
TOGA注释
hpp_pangenome_resources
人类首个 “泛基因组”旨在编目人类遗传多样性
leviosam2
Fast and accurate coordinate conversion between assemblies
miniprothint
基于miniprot筛选可信的转录本
MitoZ
MitoZ: A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes
orthology_inference2023
Inference of orthologous proteins in Drosophila genomes
PrimateAI-3D
PrimateAI-3D
SegDupAnnotation2
Count gene duplications.
SHOOT
SHOOT.bio - the phylogenetic search engine
syntplot
Scripts for plotting genome synteny based on BLAST alignment
taffy
This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
TRACCER
Convergence analysis using relative rate and correcting for phylogenetic relatedness
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