Repositories list

• HuffordLab.github.io

  Public
  Hufford Lab Website

  Ruby

  •2•1•0•0•Updated Jun 27, 2025Jun 27, 2025

• panand_genome_evolution

  Public
  repository for panand genome evolution paper

  Shell

  •0•2•0•0•Updated Jan 24, 2025Jan 24, 2025

• NAM-genomes

  Public
  Detailed bioinformatics scripts and methods used in the NAM genome paper.

  genomicsgenome-assemblybioinformatics-analysis+ 3bioinformatics-scriptsnammaize

  R

  •

  MIT License

  •30•81•2•0•Updated Jan 14, 2025Jan 14, 2025

• Inbreeding_Depression

  Public
  HTML

  •0•0•0•0•Updated Mar 24, 2024Mar 24, 2024

• Maize_WGS_Build

  Public
  Code and Data to include in WGS Build

  Nextflow

  •2•7•0•0•Updated Jan 8, 2024Jan 8, 2024

• streptochaeta

  Public
  methods for the Streptochaeta genome paper

  Shell

  •1•3•0•0•Updated Jul 31, 2023Jul 31, 2023

• Juicer_PanAnd

  Public
  modified scripts for Juicer to run effeceintly

  Shell

  •0•0•0•0•Updated May 1, 2023May 1, 2023

• Gene_Annotation_Pipeline

  Public
  Gene Annotation Pipeline

  0•2•0•0•Updated Sep 21, 2022Sep 21, 2022

• MaizeGDB_gff3_format

  Public
  script to convert GFF3 files to maizeGDB specifications

  Python

  •0•0•0•0•Updated Sep 21, 2022Sep 21, 2022

• Hufnagel_et_al._Teosinte_Hybrid_Zones

  Public
  repository for analysis pipeline and scripts for Hufnagel et al. 2021

  R

  •0•0•0•0•Updated Jun 15, 2022Jun 15, 2022

• B104

  Public
  B104 assembly and atlas project

  Shell

  •0•0•0•0•Updated Jul 19, 2021Jul 19, 2021

• GenomeQC

  Public
  R

  •7•32•0•0•Updated Dec 24, 2020Dec 24, 2020

• Wang_et_al._Demography

  Public
  Repository for the 2017 Genome Biology publication, "The interplay of demography and selection during maize domestication and expansion"

  R

  •4•17•2•0•Updated Nov 24, 2020Nov 24, 2020

• Biol462

  Public
  Course Repository for Biology 462: Evolutionary Genetics

  0•0•0•0•Updated Jun 4, 2020Jun 4, 2020

• Maize_NC358

  Public
  The repository for codes developed to generated the Maize NC358 assemblies and analyses.

  benchmarkpacbiogenome-assembly+ 4bionanomaizeread-lengthread-depth

  Jupyter Notebook

  •8•10•0•0•Updated Apr 23, 2020Apr 23, 2020

• Convergence_Domestication

  Public
  Review on the extent of convergence during domestication of cereals

  TeX

  •0•0•0•0•Updated Apr 5, 2019Apr 5, 2019

• Crop_Adaptation_Gene_Flow

  Public
  TeX

  •0•0•0•0•Updated Aug 9, 2018Aug 9, 2018

• ZeaGeneFlow_SNPChip

  Public
  TeX

  •1•1•0•0•Updated Feb 1, 2017Feb 1, 2017

• NSF_DEB

  Public
  Full Proposal: The Evolutionary Role of Hybridization and Introgression in the Genus Zea

  HTML

  •1•4•0•0•Updated Jul 24, 2015Jul 24, 2015

• Shawn_Goggins

  Public
  0•0•0•0•Updated Apr 3, 2015Apr 3, 2015

• Hufnagel_NSF_GRFP

  Public
  0•0•0•0•Updated Sep 30, 2014Sep 30, 2014