Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis
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Updated
Jul 7, 2023 - Python
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
Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format
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!
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
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