Files in jackalope

A Swift, Versatile Phylogenomic and High-Throughput Sequencing Simulator

MD5

NEWS.md README.md

NAMESPACE

DESCRIPTION

LICENSE

R/RcppExports.R R/read_write.R R/mevo.R R/haps_functions_classes.R R/aaa-classes.R R/create_haplotypes.R R/data.R R/haps_functions.R R/hts_illumina.R R/util.R R/jackalope-package.R R/hts_pacbio.R R/create_genome.R

src/Makevars.win

src/Makevars

src/ref_hap_access.cpp

src/hts_illumina.cpp

src/alter_reference.cpp

src/hts_illumina.h

src/phylogenomics.cpp

src/io.h

src/alias_sampler.h

src/RcppExports.cpp

src/pcg.h

src/util.h

src/io_fasta.cpp

src/haps_ssites.cpp

src/util.cpp

src/mutator.h

src/sub_models.cpp

src/create_sequences.cpp

src/mutator.cpp

src/io_vcf.h

src/io_ms.cpp

src/jackalope_types.h

src/hts.h

src/phylogenomics.h

src/io_vcf.cpp

src/mutator_subs.cpp

src/mutator_subs.h

src/mutator_indels.cpp

src/hts_pacbio.h

src/hap_classes.h

src/hts_pacbio.cpp

src/hap_classes.cpp

src/ref_classes.h

src/str_manip.h

src/jackalope_config.h

src/mutator_indels.h

src/mutator_type.h

inst/CITATION

inst/include/pcg/pcg_extras.hpp

inst/include/pcg/pcg_random.hpp

inst/include/pcg/pcg_uint128.hpp

inst/doc/sub-models.R inst/doc/jackalope-intro.Rmd

inst/doc/jackalope-intro.html

inst/doc/sub-models.html

inst/doc/sub-models.Rmd inst/doc/jackalope-intro.R

inst/art_profiles/HiSeq2000L100R1.txt.gz

inst/art_profiles/EmpR44R1.txt.gz

inst/art_profiles/EmpMiSeq250R1.txt.gz

inst/art_profiles/EmpR36R1.txt.gz

inst/art_profiles/MiSeqv3L250R1.txt.gz

inst/art_profiles/HiSeq2500L150R2filter.txt.gz

inst/art_profiles/MiniSeqTruSeqL50.txt.gz

inst/art_profiles/Emp100R1.txt.gz

inst/art_profiles/HiSeqXPCRfreeL150R1.txt.gz

inst/art_profiles/EmpR44R2.txt.gz

inst/art_profiles/EmpR50R1.txt.gz

inst/art_profiles/HiSeqXtruSeqL150R2.txt.gz

inst/art_profiles/Emp100R2.txt.gz

inst/art_profiles/EmpR36R2.txt.gz

inst/art_profiles/HiSeq2500L150R1filter.txt.gz

inst/art_profiles/HiSeq2500L125R2.txt.gz

inst/art_profiles/NextSeq500v2L75R1.txt.gz

inst/art_profiles/HiSeqXtruSeqL150R1.txt.gz

inst/art_profiles/EmpR50R2.txt.gz

inst/art_profiles/MiSeqv3L250R2.txt.gz

inst/art_profiles/HiSeq2000L100R2.txt.gz

inst/art_profiles/EmpMiSeq250R2.txt.gz

inst/art_profiles/EmpR75R1.txt.gz

inst/art_profiles/HiSeq2500L125R1.txt.gz

inst/art_profiles/HiSeqXPCRfreeL150R2.txt.gz

inst/art_profiles/EmpR75R2.txt.gz

inst/art_profiles/NextSeq500v2L75R2.txt.gz

build/vignette.rds

build/partial.rdb

tests/testthat.R tests/testthat/test-sequencer.R tests/testthat/test-variants_coal.R tests/testthat/test-create_mevo.R tests/testthat/test-vcf_IO.R tests/testthat/test-misc.R tests/testthat/test-fasta_IO.R tests/testthat/test-variants_other.R tests/testthat/test-R_classes.R

tests/testthat/files/ms_out.txt

tests/testthat/files/ms_out_err3.txt

tests/testthat/files/ms_out_err2.txt

tests/testthat/files/ms_out_err1.txt

vignettes/jackalope-intro.Rmd vignettes/sub-models.Rmd

data/evo_rates.rda

man/read_fasta.Rd man/haps_vcf.Rd man/evo_rates.Rd man/haps_gtrees.Rd man/write_fasta.Rd man/pacbio.Rd man/haps_functions.Rd man/create_haplotypes.Rd man/ref_genome.Rd man/haplotypes.Rd man/haps_phylo.Rd man/create_genome.Rd man/write_vcf.Rd man/jackalope-package.Rd man/indels.Rd man/haps_ssites.Rd man/illumina.Rd man/sub_models.Rd man/haps_theta.Rd

man/figures/logo.png

jackalope documentation built on May 29, 2024, 3:58 a.m.