A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

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Documentation for package ‘jackalope’ version 1.1.3

• 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.