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
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_models              Construct necessary information for
                        substitution models.
write_fasta             Write a 'ref_genome' or 'haplotypes' object to
                        a FASTA file.
write_vcf               Write haplotype info from a 'haplotypes' object
                        to a VCF file.
