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

create_genomeCreate a reference genome.
create_variantsCreate variants from a reference genome.
evo_ratesTable of evolutionary rates.
illuminaCreate and write Illumina reads to FASTQ file(s).
indelsInsertions and deletions (indels) specification
jackalopejackalope: An efficient, flexible molecular evolution and...
pacbioCreate and write PacBio reads to FASTQ file(s).
read_fastaRead a fasta file.
ref_genomeAn R6 class representing a reference genome.
site_varSpecify variation in mutation rates among sites
sub_modelsConstruct necessary information for substitution models.
variantsAn R6 class representing haploid variants from a reference...
vars_functionsOrganize higher-level information for creating variants.
vars_gtreesCreate necessary information to create variants using gene...
vars_phyloCreate necessary information to create variants using...
vars_ssitesCreate necessary information to create variants using...
vars_thetaCreate necessary information to create variants using theta...
vars_vcfCreate necessary information to create variants using a VCF...
write_fastaWrite a sequence object to a FASTA file.
write_vcfWrite variant info from a 'variants' object to a VCF file.
jackalope documentation built on Oct. 30, 2019, 11:47 a.m.