Code and plots associated with "Ancient diversity in host-parasite interaction genes in a model parasitic nematode"

Each subdirectory contains a README with descriptions of the files therein.

1_genomes

Code and files related to the first results section ("Chromosome-level reference genomes for H. bakeri and H. polygyrus")

2_divergence

Code and files related to the second results section ("The H. bakeri and H. polygyrus genomes are highly divergent")

3_heterozygosity

Code and files related to the third results section ("Heterozygosity is concentrated in distinct regions of the H. bakeri genome")

4_divergent_haplotypes

Code and files related to the fourth results section ("Hyper-divergent haplotypes are widespread in the H. bakeri genome")

5_divergent_contents

Code and files related to the fifth results section ("Ancient genetic diversity in genes associated with host-parasite interactions").

gene_annotation_files

GFF3, protein, and CDS files for the protein-coding annotations of nxHelBake1.1 and ngHelPoly1.1 reference genomes.

repeat_annotation_files

FASTA files containing the curated and initial repeat libraries for both species.