All functions

create_genome()

Create a reference genome.

create_variants()

Create variants from a reference genome.

evo_rates

Table of evolutionary rates.

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

An R6 class representing a reference genome.

site_var()

Specify variation in mutation rates among sites

sub_TN93() sub_JC69() sub_K80() sub_F81() sub_HKY85() sub_F84() sub_GTR() sub_UNREST()

Construct necessary information for substitution models.

variants

An R6 class representing haploid variants from a reference genome.

vars_functions

Organize higher-level information for creating variants.

vars_gtrees()

Create necessary information to create variants using gene trees

vars_phylo()

Create necessary information to create variants using phylogenetic tree(s)

vars_ssites()

Create necessary information to create variants using segregating sites matrices

vars_theta()

Create necessary information to create variants using theta parameter

vars_vcf()

Create necessary information to create variants using a VCF file

write_fasta()

Write a sequence object to a FASTA file.

write_vcf()

Write variant info from a variants object to a VCF file.