Sequence-to-graph mapper and graph generator

Pan-genome wide association studies

Pan-genomic sequence analysis

A Plant Presence/absence Variants Scanner and Pan-genome Construction Pipeline

SOPanG, a simple tool for pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome.

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

Rules to run Roary or PanPhlAn to build pangenome using Snakemake

Reference-free FASTQ filter for rare germline and somatic variants

Pangea: The Pan-Genome Analysis Pipeline

Pan-genomics of metagenome-assembled genomes suffers from fragmentation and incompleteness

panicmage can estimate gene gain and loss rates, the size of pan-genomes, and test for neutral evolution.

戊糖乳杆菌泛基因组分析 | Pan-genome analysis of Lactobacillus Pentosus

Pangenomic Statistical analysis in R (pasaR)

The experiments performed in State-of-the-art structural variant calling: What went conceptually wrong and how to fix it?

Comprehensive pan-genome analysis pipeline for Saccharomyces cerevisiae that integrates synteny block detection with functional annotation. Identifies core/accessory genes and conserved genomic regions across diverse yeast strains with visualization tools.

microbial pan-genome analysis

probability emitting pangenome graphs

Building Pan-Genomes based on Sequence Homology (BPG-SH) constructs and analyzes pan-genomes from multiple organisms. By leveraging sequence homology, BPG-SH integrates genomes to form a comprehensive pan-genome, enhancing our understanding of genetic diversity and evolution.