# A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

## Documentation for package ‘jackalope’ version 1.1.0

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

## Help Pages

create_genome | Create a reference genome.
create_haplotypes | Create haplotypes from a reference genome.
evo_rates | Table of evolutionary rates.
haplotypes | An R6 Class Representing Haploid Variants
haps_functions | Organize higher-level information for creating haplotypes.
haps_gtrees | Organize information to create haplotypes using gene trees
haps_phylo | Organize information to create haplotypes using phylogenetic tree(s)
haps_ssites | Organize information to create haplotypes using segregating sites matrices
haps_theta | Organize information to create haplotypes using theta parameter
haps_vcf | Organize information to create haplotypes using a VCF file
illumina | Create and write Illumina reads to FASTQ file(s).
indels | Insertions and deletions (indels) specification
jackalope | jackalope: An efficient, flexible molecular evolution and sequencing simulator.
pacbio | Create and write PacBio reads to FASTQ file(s).
read_fasta | Read a fasta file.
ref_genome | R6 Class Representing a Reference Genome
sub_F81 | Construct necessary information for substitution models.
sub_F84 | Construct necessary information for substitution models.
sub_GTR | Construct necessary information for substitution models.
sub_HKY85 | Construct necessary information for substitution models.
sub_JC69 | Construct necessary information for substitution models.
sub_K80 | Construct necessary information for substitution models.
sub_models | Construct necessary information for substitution models.
sub_TN93 | Construct necessary information for substitution models.
sub_UNREST | Construct necessary information for substitution models.
write_fasta | Write a 'ref_genome' or 'haplotypes' object to a FASTA file.
write_gtrees | Organize information to create haplotypes using gene trees
write_vcf | Write haplotype info from a 'haplotypes' object to a VCF file.