# Viral Variant Location and Diversity

## Documentation for package ‘vivaldi’ version 1.0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

add_metadata | add_metadata
af_distribution | af_distribution
arrange_data | arrange_data
dNdS_segment | dNdS_segment
example_filtered_SNV_df | Example Dataframe The DF_filt_SNVs dataframe created in the vignette
filter_variants | filter_variants
merge_replicates | merge_replicates
plot_shannon | plot_shannon
position_allele_freq | position_allele_freq
prepare_annotations | prepare_annotations
read_reference_fasta_dna | read_reference_fasta_dna
shannon_entropy | shannon_entropy
shared_snv_plot | shared_snv_plot
shared_snv_table | shared_snv_table
snpeff_info | snpeff_info
snv_genome | snv_genome
snv_location | snv_location
snv_segment | snv_segment
tally_it | tally_it
tstv_plot | tstv_plot
tstv_ratio | tstv_ratio