6184e102afac1e4331eef48adaaf4bbf *DESCRIPTION
3fb6cb5ed6ff6e1b0c1afe58f8cd6db7 *LICENSE
8fb6d11955bb1dab509ef16ac5d60db8 *NAMESPACE
2fcf9c2172b8310dbf2b220bb0167211 *NEWS.md
afe2e49669384c85959b9f99f7e6b6d4 *R/RcppExports.R
387bbb62a430255bee0403696b02b926 *R/aaa-classes.R
6ec0fc19e6b39694f1802c4b1f0629d5 *R/create_genome.R
cae7f9b75f99953014fb191a5d4a8061 *R/create_haplotypes.R
acf7d7df4619416526a6c964a700861a *R/data.R
fd870bcf6b757866adbb52b50fc95267 *R/haps_functions.R
bef5ed3c4476e3b9109fdc2fc58c71cb *R/haps_functions_classes.R
fa1fc9de1ded31af6c03f939eac042da *R/hts_illumina.R
746179b2b813e882cae01a5970c90407 *R/hts_pacbio.R
7db14fd38c253e0136fc0ebd9e12d9d9 *R/jackalope-package.R
fa295b393e18465118be56d558d89567 *R/mevo.R
6867f495b7dab8d201fcfda6dee55bfc *R/read_write.R
8c3c2d107231a0aded1cd65b0d9b1215 *R/util.R
dbab8c7035c929ad1d55ee232020fcee *README.md
7080893e02c49cd296d4424b9be55069 *build/partial.rdb
2d7f250a70ddb07ea833965bba7060a0 *build/vignette.rds
e53b1cad633ef60ce4e23042d446a29e *data/evo_rates.rda
f071d7f1c3f9f4fa2f4efe2559bd7caa *inst/CITATION
4b3be45e2fbc04196fd1eff2228fa45d *inst/art_profiles/Emp100R1.txt.gz
f4763415cbed89bfb7eb5658992daacd *inst/art_profiles/Emp100R2.txt.gz
a4632056ba1040b7cb9fc1735f601d6a *inst/art_profiles/EmpMiSeq250R1.txt.gz
66c1d18c6677bbd341c6cda83bd342ce *inst/art_profiles/EmpMiSeq250R2.txt.gz
d45f4296935c570601448e703c986da3 *inst/art_profiles/EmpR36R1.txt.gz
51f58b1912f79b0ed100998e393fe06b *inst/art_profiles/EmpR36R2.txt.gz
9f34c0fb1ea1491e7bebc36e72cd2cc4 *inst/art_profiles/EmpR44R1.txt.gz
4108940e1d7800e035d3a45900c3b8ca *inst/art_profiles/EmpR44R2.txt.gz
ebe01238026fdec87e45f1bc7d4d8f1d *inst/art_profiles/EmpR50R1.txt.gz
192c2c1ae0a723450f1eaf8f2d3f3b86 *inst/art_profiles/EmpR50R2.txt.gz
05e62ec8bf2b245bcabd2cd424c5348c *inst/art_profiles/EmpR75R1.txt.gz
cb9f9e83fc78d9154af6cda12bd1b5e4 *inst/art_profiles/EmpR75R2.txt.gz
a5690832c8a975aea89d0148df696be3 *inst/art_profiles/HiSeq2000L100R1.txt.gz
761c6b0d74a0238210d5555609f3669c *inst/art_profiles/HiSeq2000L100R2.txt.gz
61c6ecd98ed4c12010a67f4885d8272d *inst/art_profiles/HiSeq2500L125R1.txt.gz
be5a1fc13503e15cd320a179c93b14c1 *inst/art_profiles/HiSeq2500L125R2.txt.gz
28f6197cbd4a43cefc34e18458e0b3ba *inst/art_profiles/HiSeq2500L150R1filter.txt.gz
c242e6705b7b70f83eae1a24f739f949 *inst/art_profiles/HiSeq2500L150R2filter.txt.gz
a26c411e6869a12a08d14baff32f2320 *inst/art_profiles/HiSeqXPCRfreeL150R1.txt.gz
5d5271b791b040a2c9b7b805182a1c05 *inst/art_profiles/HiSeqXPCRfreeL150R2.txt.gz
42672cd4d5e32165097a1a317144137f *inst/art_profiles/HiSeqXtruSeqL150R1.txt.gz
e46da072ce77f96968ae98cd1ccd0c2a *inst/art_profiles/HiSeqXtruSeqL150R2.txt.gz
78e9b14fcb2d00934aa20c2ae3b46a9a *inst/art_profiles/MiSeqv3L250R1.txt.gz
487cbcc8577689a6fe759d8808ae73e0 *inst/art_profiles/MiSeqv3L250R2.txt.gz
e9a5aa103f17860afd48ab3a3e6cd897 *inst/art_profiles/MiniSeqTruSeqL50.txt.gz
de1f2d814d8c622be6a4c89aa4c0ea85 *inst/art_profiles/NextSeq500v2L75R1.txt.gz
443281230cb8b598f3711e04d1116ac3 *inst/art_profiles/NextSeq500v2L75R2.txt.gz
0556d946902fad998efca27732cc4ebd *inst/doc/jackalope-intro.R
5a99c0ca99183b1af81998ac6d30846b *inst/doc/jackalope-intro.Rmd
5678bf95e387a0023ac7e76787f32f15 *inst/doc/jackalope-intro.html
858fb5065cfb9c6896feea77eaae58d9 *inst/doc/sub-models.R
447e6355351d1c0fdcc59b40356b869a *inst/doc/sub-models.Rmd
384fd4a5d84373a72733ab0eb919fe28 *inst/doc/sub-models.html
7abf0105712a40bf323b7e0cf85524ee *inst/include/pcg/pcg_extras.hpp
148b36a5b86f436ed4f455997041b262 *inst/include/pcg/pcg_random.hpp
d68210ec9fe1574857a10f1846309cdb *inst/include/pcg/pcg_uint128.hpp
86338c27c4daa8e7eab5e17fa6c29ba9 *man/create_genome.Rd
5e45e446b3aecf998c9a023da53ef43e *man/create_haplotypes.Rd
5d584be1f7de003cec695a5586176b7d *man/evo_rates.Rd
a9d6f21cd4cf93cbc70b05dff9b02eb3 *man/figures/logo.png
2c675e6fc03ba1fce4d1c957e5afdf8c *man/haplotypes.Rd
235494a6622524e0d3375df7b095c3d9 *man/haps_functions.Rd
59f80458c77b8594b02c90b5762a33fb *man/haps_gtrees.Rd
572b9ec7dccefc5594d67e26f5b589b8 *man/haps_phylo.Rd
d351d2115bd62e335c38280784f69f10 *man/haps_ssites.Rd
fc9b80faa3cb72338460c730b39c3685 *man/haps_theta.Rd
c99ea5dcb564c74d47682d45b5750106 *man/haps_vcf.Rd
5cf349a10ff42f4c3a8554f5ce8f9d2c *man/illumina.Rd
398218b2674dba5f6ecb7db4677a1044 *man/indels.Rd
ead34c1256d36153fb46a6d8bb0a0c52 *man/jackalope-package.Rd
0dc26c020d39199d3b03fad13aa28337 *man/pacbio.Rd
d01123e5fcebe78b8dfacce56fbe01f1 *man/read_fasta.Rd
253c84cb9cb851d5d07a00f116898caa *man/ref_genome.Rd
1b74bfcca1f9fc824090d37e8f373c8e *man/sub_models.Rd
64fc61dfaab66d39c0367ed1d4937b83 *man/write_fasta.Rd
9ddc631a1698e149456b768b29edee90 *man/write_vcf.Rd
b118498934631825bc282d55f77889bc *src/Makevars
e3a48d806e095becc9c5b1ffbc1ac029 *src/Makevars.win
e0d580a3621818564ba838e2c51541b2 *src/RcppExports.cpp
b56affc38e567e55089207aa43d5a6ed *src/alias_sampler.h
bad4a30444598ccea69d174a4f14aa8c *src/alter_reference.cpp
44c90b0a7281d70ad31ce69440612d69 *src/create_sequences.cpp
0c29df5388a0847f9e882ef7961485fc *src/hap_classes.cpp
2b88d6d4c7d161af76230a800f808796 *src/hap_classes.h
3c64f5071fb7929041e653598412a5dd *src/haps_ssites.cpp
8ff99b31fd393ec2e47b5a9348b595b0 *src/hts.h
a1f75512361ec03416926a3a27b2e576 *src/hts_illumina.cpp
1ae0b37fd9eabc59d68371442a999517 *src/hts_illumina.h
2188e1e280de4e0e027626c1233faae8 *src/hts_pacbio.cpp
1379e66879ee1f76da69b051240b6403 *src/hts_pacbio.h
dfb2bf1c75bf3574629c4dd48510060a *src/io.h
bdb0c9b36dc6c620fdddff5ff4f4e804 *src/io_fasta.cpp
1bed478767a1d7e4339162ad9215bab2 *src/io_ms.cpp
73b1810ab7a77b3efde5456cc2abdec1 *src/io_vcf.cpp
d80c0e674fc35dfd6223045f5a44601b *src/io_vcf.h
8af5036bb551622517d23156d6211499 *src/jackalope_config.h
64b40465b4b04ce6f4d69dd626b0b063 *src/jackalope_types.h
28420638660c2048a2366c19e90de76e *src/mutator.cpp
c0a90b564c8b7c9416ddd8ad31913e6e *src/mutator.h
3d0cd26e621f67124212b3e756346e20 *src/mutator_indels.cpp
803e6b37fae1afb58b39b9bc22d61e94 *src/mutator_indels.h
7ad477163f94f1cd962f6733b25075ec *src/mutator_subs.cpp
6c162e109ba4f1f9c43f9b73f5f021e5 *src/mutator_subs.h
dc1609f14a533110b540578036a3b265 *src/mutator_type.h
4b66895707ae12293f3ffc52fe1d5f65 *src/pcg.h
673daa99cef037bb63a4428cdb31e806 *src/phylogenomics.cpp
238be1d340c01b18dad700ed6421c02a *src/phylogenomics.h
db4d7fed5df4215a56e7fb3b4178b8d5 *src/ref_classes.h
6e0fdb32a2902f16b1a03f036c637dd9 *src/ref_hap_access.cpp
07c35e6a53350a5f6c45ce20a457fb51 *src/str_manip.h
f7013a98f44d2960b5e18022efc085e9 *src/sub_models.cpp
c14dcf78fae19b87893c7a1a0777cd24 *src/util.cpp
f6bb6836f175f6d488a01db7175e20c7 *src/util.h
0969a755078166e21e9e226d5162455d *tests/testthat.R
0a7a240a40f3e59d84ae1c39647d4182 *tests/testthat/files/ms_out.txt
0293f572e798579a9ed426ccdddc17b7 *tests/testthat/files/ms_out_err1.txt
a7310cb2e4b6f5c80f366101b3af1928 *tests/testthat/files/ms_out_err2.txt
f175b624a8afc2a0bdaa890487c75cf9 *tests/testthat/files/ms_out_err3.txt
fb918a415e07f1f7c2678da3327378b5 *tests/testthat/test-R_classes.R
e5a1ad5df6a8c149a6498dc5be096939 *tests/testthat/test-create_mevo.R
badd85a451f4d26ec269c0b505573219 *tests/testthat/test-fasta_IO.R
bb4e5bfc245e9f7281ab027304844c53 *tests/testthat/test-misc.R
8c185739e4c2cc03b0ed3aae8cea66c9 *tests/testthat/test-sequencer.R
c2c822772a25dacee1088692a2c6dae1 *tests/testthat/test-variants_coal.R
75fc034bc9ef5ce12e30192447cb1552 *tests/testthat/test-variants_other.R
2f9fb0f2c0b229bffde78ba5e54ff886 *tests/testthat/test-vcf_IO.R
5a99c0ca99183b1af81998ac6d30846b *vignettes/jackalope-intro.Rmd
447e6355351d1c0fdcc59b40356b869a *vignettes/sub-models.Rmd
