All functions

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() write_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_JC69() sub_K80() sub_F81() sub_HKY85() sub_F84() sub_TN93() sub_GTR() sub_UNREST()

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.