Man pages for jackalope
A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

create_genomeCreate a reference genome.
create_haplotypesCreate haplotypes from a reference genome.
evo_ratesTable of evolutionary rates.
haplotypesAn R6 Class Representing Haploid Variants
haps_functionsOrganize higher-level information for creating haplotypes.
haps_gtreesOrganize information to create haplotypes using gene trees
haps_phyloOrganize information to create haplotypes using phylogenetic...
haps_ssitesOrganize information to create haplotypes using segregating...
haps_thetaOrganize information to create haplotypes using theta...
haps_vcfOrganize information to create haplotypes using a VCF file
illuminaCreate and write Illumina reads to FASTQ file(s).
indelsInsertions and deletions (indels) specification
jackalope-packagejackalope: A Swift, Versatile Phylogenomic and...
pacbioCreate and write PacBio reads to FASTQ file(s).
read_fastaRead a fasta file.
ref_genomeR6 Class Representing a Reference Genome
sub_modelsConstruct necessary information for substitution models.
write_fastaWrite a 'ref_genome' or 'haplotypes' object to a FASTA file.
write_vcfWrite haplotype info from a 'haplotypes' object to a VCF...
jackalope documentation built on May 29, 2024, 3:58 a.m.