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

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

Phasing and scaffolding polyploid genomes based on Pore-C or Hi-C.

R package for random-effect multiple QTL mapping in autopolyploids

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

Method for rescuing collapsed contigs.

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

triploid SMC inference method

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

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

🌺 Short pipeline for counting number of clusters across .sam files

Preliminary mapping and SDM