maize_nlrome

This repository contains scripts used for phylogenetic, sequence diversity, and genomic feature analysis of the Zea mays NLRs from long-read NAM genomes. The scripts are integrated via a snakemake file which also relies on hmmmer, mafft, and raxml. The features directory includes the scripts associated with analysis of NLR expression and methylation.

Name		Name	Last commit message	Last commit date
Latest commit History 39 Commits
Archive		Archive
features		features
.gitignore		.gitignore
DomainDiagrams_sm.R		DomainDiagrams_sm.R
Extract_LRRpred_sm.R		Extract_LRRpred_sm.R
Maize_AF_Chimera_Setup.R		Maize_AF_Chimera_Setup.R
Maize_Karyogram.R		Maize_Karyogram.R
Maize_NLRome_CladeAnalysis.R		Maize_NLRome_CladeAnalysis.R
Minimal_Chimera_Entropy_Script.R		Minimal_Chimera_Entropy_Script.R
README.md		README.md
Zm_NLRome.Rproj		Zm_NLRome.Rproj
Zm_NLRome_ChromStrip.R		Zm_NLRome_ChromStrip.R
Zm_NLRome_InitialAssignment_sm.R		Zm_NLRome_InitialAssignment_sm.R
Zm_NLRome_PrintInitClades.R		Zm_NLRome_PrintInitClades.R
Zm_NLRome_PrintRefinedClades.R		Zm_NLRome_PrintRefinedClades.R
Zm_NLRome_Refinement_sm.R		Zm_NLRome_Refinement_sm.R
reduce_pfam.R		reduce_pfam.R

krasileva-group/maize_nlrome

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maize_nlrome

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