ae9e9df8da6fb14e2f6fa4f06468d3ba *DESCRIPTION
155ed49c9888b26ff76e538bb90568b2 *LICENSE
8e932914210b5c1529fc21becce5f552 *NAMESPACE
793148e8bd8fd0a76cff430465ed21ff *R/all-classes.R
9af706cae7a199a8c45db880b9c9a685 *R/phylotaR.R
8b6a4d871462174b9ff3b272b6825396 *R/pipeline-tools.R
e48a37b087ca9f08920709b6ac87c0b9 *R/pipeline.R
04bcb5fd2761f1002a7ba9962f34ac91 *R/stage1-tools.R
6703d1f360c5a1bc666cabcbcd7f3502 *R/stage1.R
44f76e592bfda4157c6053c1460973c9 *R/stage2-tools.R
27e1e4dd47fcc7c26980b55cc0b1279b *R/stage2.R
a5d60d92ce61f95ba5e2e7d6a32dab7c *R/stage3-tools.R
8a6097099fa08fdf9d562fc67c3fe591 *R/stage3.R
242d29e63eae99f4dbd08f0c9cef9f73 *R/stage4-tools.R
dd0a74f8057f6569356f7bdd4c2edab3 *R/stage4.R
28f51c9644ef6f3956dee7123de4e00f *R/tools-api.R
c9be066ab257573b1d861fe304add3fa *R/tools-blast.R
84182404a1e055f7a6ca0c5cf793fa84 *R/tools-cache.R
0446cb721559a4ab0567aef3ed080c4f *R/tools-entrez.R
2618d238e83b71171592b9e8e9ebf997 *R/tools-log.R
e8ed18fa79f6f53ece415e4f1b0985a0 *R/tools-sqs.R
4d14588f0f7aa0c7550310457c2b6b6d *R/tools-system.R
9fb2e2412f91a61141124824a1fcf3c9 *R/tools-tests.R
5070fe193a7c72ddc6ecc17fa35c46b1 *R/tools-txdct.R
5e2885978dc2a7c221358f080b69b2ea *R/user-calc.R
1c5380f7c4e07b1d9ca1c90aef663476 *R/user-drop.R
b2cff80104c93334eb06339dc2231afc *R/user-get.R
b178de1ae18d612c093b718b8e693077 *R/user-special.R
53259638a032559a64607d63090f61be *README.md
61feda5fb6fff4df36e612ac0ddc1c84 *build/vignette.rds
1b03fad89613b9041554c62a30245c94 *data/aotus.rda
a884a2e6a447f4ed9630486484a7e1f2 *data/bromeliads.rda
e7c249399d732a42160584ba0c46f639 *data/cycads.rda
30d73bc00c3f49283dc8ffa755082345 *data/datalist
be09e89841dcef3e23ba76530e1dee1c *data/dragonflies.rda
ee053fdc5a2ceeccd591009136e59f01 *data/sturgeons.rda
b619480ff016dd1de48ddde0d99be9af *data/tardigrades.rda
5eb53887b06ca3a18494e81db8e9b3a6 *data/tinamous.rda
7d0f8d8e851130f199786c2e4ec07101 *data/yeasts.rda
22ead775d2a5939acbeeca1775afc6ea *inst/doc/phylotaR.R
5e543f384cb37fa97bf8490bfe769824 *inst/doc/phylotaR.Rmd
5c2ac5acddeb38ff2d5713777c05a1a3 *inst/doc/phylotaR.html
22afa6bd6234b2f31a6cc417132a2342 *man/ClstrArc-class.Rd
52f9f7d9f0f0b4ef4454654203c7d11d *man/ClstrRec-class.Rd
7421886839e1d8bb9e26ac693edc2105 *man/Phylota-class.Rd
8b91bca9be1b1c6b597654b948321533 *man/SeqArc-class.Rd
e82eb521bdc489f048672768cd6f3155 *man/SeqRec-class.Rd
9d487ae1c57129134d62b84838821c2e *man/TaxDict-class.Rd
7a640bbc15681832849108b469b21334 *man/TaxRec-class.Rd
31e79c46fbe24a1420c12493dc74c25b *man/aotus.rd
e9ed8510a6d2fcf9959d8f3e4e0e7caa *man/batcher.Rd
3259d1b2a960aa9a0415e242bcf9057b *man/blast_clstr.Rd
328f5b5a3afe8845c891c7c809932410 *man/blast_filter.Rd
05e75c4185665d60593c453d8d8e4421 *man/blast_setup.Rd
7a6e2f2be80fa54596c867d6f4d2621e *man/blast_sqs.Rd
5063db30ba1985cd2d5efb712d4146ab *man/blastcache_load.Rd
3a32544682594b2964b27c98c3b828c1 *man/blastcache_save.Rd
71d381072cd107f37703f99b6925e3e8 *man/blastdb_gen.Rd
cf51b8dd8182659edf40778a5ba67434 *man/blastn_run.Rd
07e974ee306618ce260d07bf50d5a0c3 *man/bromeliads.rd
da90e855b88805b7d39f5c039fd66758 *man/cache_rm.Rd
b4490d27db5e4c6d6553d2cfe8def4ee *man/cache_setup.Rd
422c22e65dcbe3cdc1b647e785ba6c97 *man/calc_mad.Rd
772721076b7839a1949d5ed5b2e62e2b *man/calc_wrdfrq.Rd
5e35a3d4ddb63a301593a32e099bb8fd *man/clade_select.Rd
97a9bbdd015d017cb8950188419f22ea *man/clstr2_calc.Rd
e77746937c6ac6397a3de7e3022bfaa3 *man/clstr_all.Rd
fdb2822a66db25872b110a3713debc22 *man/clstr_direct.Rd
002e68c1cae6fc28ea30344cf689f6e4 *man/clstr_sqs.Rd
e95b2ab29811ef229f7bee88ca0c5b10 *man/clstr_subtree.Rd
741a2bcb9943ef8f971c6dcc06c038f5 *man/clstrarc_gen.Rd
3a6a09fa49d4392c739d6ed9b34dd1fa *man/clstrarc_join.Rd
f671664ff3e0ceebf477c43053f602b6 *man/clstrrec_gen.Rd
4b39155b8b2027380827fe950cb9fc44 *man/clstrs_calc.Rd
ee50c1e5938041b6ca10364f094ee9d2 *man/clstrs_join.Rd
aab56cbcb8ef581e50c2f24cc6411342 *man/clstrs_merge.Rd
23d1e87141092407ab46c69e8e3604e2 *man/clstrs_renumber.Rd
03980b98cca589317aa7be51f689797f *man/clstrs_save.Rd
ea92eb7a12220ae25cab024c36e26fdf *man/clusters2_run.Rd
5d09bec6c3e7e6c40abeb945623d780e *man/clusters_run.Rd
f84ceb69b8b910a0fc56e898213bcb4d *man/cmdln.Rd
4a0cf152003ee8d825ce169e2faa5ac1 *man/cycads.rd
ed7d5623a744d6846437415cfed7e12f *man/descendants_get.Rd
4c8c33303b4b119da4009c63677cde7d *man/download_obj_check.Rd
ca7cb8e9e58fcc4f74614d1614fd2de5 *man/download_run.Rd
1518098213d6cd3ddf7a4a3d9ba93fa4 *man/dragonflies.rd
6e8da91ccd12b768ec2f2728a78b3bf0 *man/drop_by_rank.Rd
a393d55309fe0cc31ed3432c9da353ce *man/drop_clstrs.Rd
3ec27591ea7ddee8b9aa278c6dcc07d5 *man/drop_sqs.Rd
d3fb3cb438e8d99a708b50a9ebb27a28 *man/error.Rd
c6d4febfceeffe8df3b4ca747ead01fc *man/get_clstr_slot.Rd
c946fc42b63c40b66e0311378f64e298 *man/get_nsqs.Rd
fb99269941b8bec1e74abc7f02ab2b12 *man/get_ntaxa.Rd
a0439d5b50797f89d77e3b6964222a52 *man/get_sq_slot.Rd
0b41a4d70208d73cd202b8b484c4526e *man/get_stage_times.Rd
53b2085a1dc6e00a2de4ec6d6dfe1570 *man/get_tx_slot.Rd
53e01a5a70adb9d8dc6b52af8c16d2a7 *man/get_txids.Rd
dd1ca2d755de71836317a18d98a26888 *man/hierarchic_download.Rd
6fa600afcd2ab7166dd8eac9d393180d *man/info.Rd
238fefa65618d352206c5a3ef98d0bb5 *man/is_txid_in_clstr.Rd
a75e1fb1cd2517d1cab08ba736f4fb61 *man/is_txid_in_sq.Rd
fb04b9b145daf871c4d0e31d8d17ce8d *man/list_clstrrec_slots.Rd
7cd3018d82138b6e5ff344558ba9a901 *man/list_ncbi_ranks.Rd
92dc8fb8cc5970811167f0ab57fbf89f *man/list_seqrec_slots.Rd
7975333c2af8f06980c64ed455e3a3ef *man/list_taxrec_slots.Rd
4ae4106d46660f3755dbd27beded484a *man/mk_txid_in_sq_mtrx.Rd
003e61633a064c6b62511ed0c63ccea1 *man/ncbicache_load.Rd
ae43c4d66ab5e42d86a6278a575a7781 *man/ncbicache_save.Rd
2ebbd7849009fa88915542cae100b716 *man/obj_check.Rd
890db5d4465f9a8bc4e8e90997b65ae5 *man/obj_load.Rd
5ddd68c6702f3e2843fbfed42a556b73 *man/obj_save.Rd
6722afa7518804aa6ada8bd5d134397d *man/parameters.Rd
870d61082659b2e36c91feda8690bf53 *man/parameters_load.Rd
dc12cc24a64b484a60cb0220e818836a *man/parameters_reset.Rd
2b77bf21729da4dae55669e991f4ea90 *man/parameters_setup.Rd
99535ab3ed97d6c731269a3cffcbb907 *man/parent_get.Rd
3f96f3cc3283e7c936bc6380bfae0373 *man/plot_phylota_pa.Rd
65c333592d0c09d1783cead13db8c7bc *man/plot_phylota_treemap.Rd
5ee1754ef3a03b129fcd9e62effada19 *man/progress_init.Rd
0a29a7b5d7dc681c02e97b87a832075b *man/progress_read.Rd
16f4cc1426475d478b5ef58bbad1ef16 *man/progress_reset.Rd
806959795ca3797428bac7301edd2b08 *man/progress_save.Rd
49568194d1a175edd095e6a4fb0a1a52 *man/rank_get.Rd
211958033d1a3503e5821449e7dccb80 *man/read_phylota.Rd
bbc6667ce41fa947581a65c203956db0 *man/reset.Rd
36d5b402229dfeb873abfc893331c4b9 *man/restart.Rd
3e7bcf2535ad3a3cccb364638278b0c3 *man/run.Rd
8c780cbf0f3a6cbb0bb18c66b53794b2 *man/safely_connect.Rd
77a5b6d2f56be6f0bf23f94600231770 *man/search_and_cache.Rd
d095fc1791b0f8ef446a400619ac2e8e *man/searchterm_gen.Rd
428575ba01553653ea678a4a18bbd04c *man/seeds_blast.Rd
091886cd532c15f1c85731587abe44f3 *man/seq_download.Rd
c14c0b9fe06220bc4a6782c271fade76 *man/seqarc_gen.Rd
3f94116db849ad2ab71f05b364434bf9 *man/seqrec_augment.Rd
afae4b6015983502231f5dd39cf7f40f *man/seqrec_convert.Rd
e55fc9afb4811b35b720024202f6dd71 *man/seqrec_gen.Rd
75478b02d2c98e1190488b853fe3488c *man/seqrec_get.Rd
19db7482d386f76bf4d873758a4a7b07 *man/setup.Rd
2d80b1b43ae48aac69aa890a259ce99c *man/sids_check.Rd
4e0e13ad3a1cba1b39df0558fe391ad3 *man/sids_get.Rd
ab54383adc238daaf4df34f77be1e554 *man/sids_load.Rd
25e8f2c3e0585039912047ed8067f4b5 *man/sids_save.Rd
d6fb008db9b96750a39543dc1b3f57b5 *man/sqs_count.Rd
0537396e01ad9d388ce3daa887f058fa *man/sqs_load.Rd
a2ae72af954ba185e1c50b3e611281ba *man/sqs_save.Rd
ca208370972065263d4167236b374769 *man/stage_args_check.Rd
be9c243b9165e80e6dc20a52620c6922 *man/stages_run.Rd
2fdd1cc10c1d24eef7e06f2c0dbef609 *man/sturgeons.rd
203a64f4e9aea95be6b072b80cbd3935 *man/summary_phylota.Rd
273a8c30ffcfb96695d248690ae20ccd *man/tardigrades.rd
96813a91d032aed98178b0b943ba99b4 *man/tax_download.Rd
f2d9bce064a835091c69e97daf2cfe34 *man/taxdict_gen.Rd
84c325e2f4f12b237179e53a7423a0f0 *man/taxise_run.Rd
119f38c9aa51c9870f0960cec6f02b27 *man/taxtree_gen.Rd
d27c7911b2d9da098ab02f3fe66aa221 *man/tinamous.rd
5065dd5b3927367750bcf3e4f4417bc9 *man/txids_get.Rd
6c512ac872aee11fe7d3a82faab8aff0 *man/txnds_count.Rd
80e2c0a8ad19c7067dd29fd14d7a4cb2 *man/update_phylota.Rd
26299f52b2d28699f9b6f9d474530b97 *man/warn.Rd
05b9837a3745a96e76622bfa1e7eca56 *man/write_sqs.Rd
66b6540ecb752f827c3553d2cc828ef8 *man/yeasts.rd
10664b7f9ec8364cd9530badf8519779 *tests/test-all.R
f1ba3a316264182878200dd37ee8a819 *tests/testthat/data/api/xml_timeout.rda
cb329060c82ffd06e37d38aec30fb8dc *tests/testthat/data/blast/README
288e8b4f933cb4db4b031ace6750120c *tests/testthat/data/blast/blast_res.rda
3f5093c3fda9d58c723f195bf3d6fb96 *tests/testthat/data/blast/testblstn
034ce673482cf6de07f9d98d6cb25fd0 *tests/testthat/data/blast/testdb.nhr
9b898c26f76e711f59c1ce5b65fd452c *tests/testthat/data/blast/testdb.nin
4e930843b111259887723960b4256bbb *tests/testthat/data/blast/testdb.nsq
fdd35258d45a596678519e9fca6aa53e *tests/testthat/data/clstrarc.rda
e10e49560c0b3ad580103ee5122540e4 *tests/testthat/data/raw_seqrecs.rda
80a0e02c13cb45eb9e2f01e6fcfdb064 *tests/testthat/data/raw_txrecs.rda
03a58f2a5bcd8b477c34d38da449ff09 *tests/testthat/data/sqrecs.rda
a5c0e9b55199f28dd7299fe833b6783d *tests/testthat/data/taxonomy/txids_records.RData
7d68a43b2f1b86298a4ad804e6efda0e *tests/testthat/data/txdct.rda
3f99481c4194ce11af5a7206e5eec98f *tests/testthat/data/txrecs.rda
904bb0faf4ae3186704a5563a38d6199 *tests/testthat/test-all-class.R
8204411848ff5e0aa4edd942c18033e3 *tests/testthat/test-phylotar.R
51880ab5d267f93b6cd8bbdddca7af3a *tests/testthat/test-pipeline.R
358b692f9e4248b39cd3df3d766eb699 *tests/testthat/test-stage1-tools.R
e5409b8a1ceb916d86912f5b05963cad *tests/testthat/test-stage1.R
fcb04361e8cf33f2b4d71756fac83c4b *tests/testthat/test-stage2-tools.R
6edd9dc485f01445b6b8ec6483dbb6b9 *tests/testthat/test-stage2.R
f582d308c31fbd4af96481e2842b1136 *tests/testthat/test-stage3-tools.R
53b6693eaaab4327d610770a7f44403d *tests/testthat/test-stage3.R
069b90c30f2135f9dbc4bed2274372e7 *tests/testthat/test-stage4-tools.R
04fa9bed465c8331388341495547ac92 *tests/testthat/test-stage4.R
e3c0da247df2d27879bdf45f373323b4 *tests/testthat/test-tools-api.R
090b130951baeff7749cb4e3455a3a44 *tests/testthat/test-tools-blast.R
6887c29c4fe86b66f30be0fefc7bf1a3 *tests/testthat/test-tools-cache.R
18706d8f2390926352b5d9fb27c4043c *tests/testthat/test-tools-entrez.R
5f680254372421325c5e035ed25c8765 *tests/testthat/test-tools-log.R
88f80c3a9a89434c73170a1cb9714e0b *tests/testthat/test-tools-pipeline.R
09b0fadb0920d665f0eec25182337216 *tests/testthat/test-tools-sqs.R
a608217c29ad44c1a219b7518d7bde63 *tests/testthat/test-tools-system.R
1627bd2e6403ba13d2c54201aff8f9c9 *tests/testthat/test-tools-test.R
ec70e762c9510b0475b923e265205575 *tests/testthat/test-tools-txdct.R
d39985b540c7afe1fcea826dbe1836db *tests/testthat/test-user-calc.R
585037795e5a913b255eb25afac4d8ac *tests/testthat/test-user-drop.R
6bb5a8ea445b7f8a413de3dcb5c238cc *tests/testthat/test-user-get.R
2167c52102464b736e87c9444b3fba5d *tests/testthat/test-user-special.R
5e543f384cb37fa97bf8490bfe769824 *vignettes/phylotaR.Rmd
