polyploid

Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on 3C-based data (Pore-C, CiFi, Hi-C, Omni-C).

A KMER-based genome-wIde Assocation testing approach on polyploids

Genome scaffolding based on HiC data in heterozygous and high ploidy genomes

Ploidy agnostic phasing pipeline and algorithm

Genetic maps in autopolyploids

Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format

C-Studio is a desktop app for visualizing and editing chromosome-scale genome assemblies with AGP layouts, 3D contact maps, synteny, and assembly-graph evidence.

R package for random-effect multiple QTL mapping in autopolyploids

Method for rescuing collapsed contigs.

Quantitative and population genetics analyses of populations, pools, half-sib/full-sib families, and polyploids

Nextflow pipeline to find syntelogous genes in phased genome assemblies of polyploid plants

This repo is deprecated. Use https://github.com/plantarum/flowPloidy instead!

This repository contains the main codes used in the manuscript: "Oryza genome evolution through a tetraploid lens"

Polyploid-aware VCF to dosage matrix conversion

triploid SMC inference method

This repository serves to document, share, and collaborate on scripts used in the University of Arkansas fruit breeding lab.

This is a modified version of C-Phasing -- zgtools

This repository hosts codes and analytic procedures for the article "The recombination landscape and multiple QTL mapping in a Solanum tuberosum cv. ‘Atlantic’-derived F1 population" by Pereira et al. (2020)

Automated processing and haplotype inference for double-barcoded PCR amplicons