Files in ropensci/phylotaR
Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
.Rbuildignore
.github/CONTRIBUTING.md
.github/issue_template.md
.github/pull_request_template.md
.github/workflows/r-check.yml
.gitignore
CONTRIBUTING.md
CRAN-SUBMISSION
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/a.R
R/all-classes.R
R/data.R
R/phylotaR.R
R/pipeline-tools.R
R/pipeline.R
R/stage1-tools.R
R/stage1.R
R/stage2-tools.R
R/stage2.R
R/stage3-tools.R
R/stage3.R
R/stage4-tools.R
R/stage4.R
R/tools-api.R
R/tools-blast.R
R/tools-cache.R
R/tools-entrez.R
R/tools-log.R
R/tools-sqs.R
R/tools-system.R
R/tools-tests.R
R/tools-txdct.R
R/user-calc.R
R/user-drop.R
R/user-get.R
R/user-special.R
README.md
_pkgdown.yml
data/aotus.rda
data/birds.rda
data/bromeliads.rda
data/cycads.rda
data/dragonflies.rda
data/mammals.rda
data/plants.rda
data/sturgeons.rda
data/tardigrades.rda
data/tinamous.rda
data/yeasts.rda
demos/demo_run.R
examples/calc_mad.R
examples/calc_wrdfrq.R
examples/clstrarc-class.R
examples/clstrrec-class.R
examples/clusters2_run.R
examples/clusters_run.R
examples/download_run.R
examples/drop_by_rank.R
examples/drop_clstrs.R
examples/drop_sqs.R
examples/get_clstr_slot.R
examples/get_nsqs.R
examples/get_ntaxa.R
examples/get_sq_slot.R
examples/get_stage_times.R
examples/get_tx_slot.R
examples/get_txids.R
examples/is_txid_in_clstr.R
examples/is_txid_in_sq.R
examples/parameters_reset.R
examples/phylota-class.R
examples/plot_phylota_pa.R
examples/plot_phylota_treemap.R
examples/read_phylota.R
examples/reset.R
examples/restart.R
examples/run.R
examples/seqarc-class.R
examples/seqrec-class.R
examples/setup.R
examples/taxdict-class.R
examples/taxise_run.R
examples/taxrec-class.R
examples/write_sqs.R
justfile
logo.png
man-roxygen/lvl.R
man-roxygen/ps.R
man/ClstrArc-class.Rd
man/ClstrRec-class.Rd
man/Node-class.Rd
man/Phylota-class.Rd
man/SeqArc-class.Rd
man/SeqRec-class.Rd
man/TaxDict-class.Rd
man/TaxRec-class.Rd
man/TreeMan-class.Rd
man/TreeMan-to-phylo.Rd
man/TreeMen-class.Rd
man/TreeMen-to-multiPhylo.Rd
man/addClade.Rd
man/addNdmtrx.Rd
man/addTip.Rd
man/aotus.Rd
man/batcher.Rd
man/birds.Rd
man/blast_clstr.Rd
man/blast_filter.Rd
man/blast_setup.Rd
man/blast_sqs.Rd
man/blastcache_load.Rd
man/blastcache_save.Rd
man/blastdb_gen.Rd
man/blastn_run.Rd
man/blncdTree.Rd
man/bromeliads.Rd
man/cTrees.Rd
man/cache_rm.Rd
man/cache_setup.Rd
man/calcDstBLD.Rd
man/calcDstMtrx.Rd
man/calcDstRF.Rd
man/calcDstTrp.Rd
man/calcFrPrp.Rd
man/calcNdBlnc.Rd
man/calcNdsBlnc.Rd
man/calcOvrlp.Rd
man/calcPhyDv.Rd
man/calcPrtFrPrp.Rd
man/calc_mad.Rd
man/calc_wrdfrq.Rd
man/checkNdlst.Rd
man/checkTreeMen.Rd
man/clade_select.Rd
man/clstr2_calc.Rd
man/clstr_all.Rd
man/clstr_direct.Rd
man/clstr_sqs.Rd
man/clstr_subtree.Rd
man/clstrarc_gen.Rd
man/clstrarc_join.Rd
man/clstrrec_gen.Rd
man/clstrs_calc.Rd
man/clstrs_join.Rd
man/clstrs_merge.Rd
man/clstrs_renumber.Rd
man/clstrs_save.Rd
man/clusters2_run.Rd
man/clusters_run.Rd
man/cmdln.Rd
man/cycads.Rd
man/descendants_get.Rd
man/download_obj_check.Rd
man/download_run.Rd
man/dragonflies.Rd
man/drop_by_rank.Rd
man/drop_clstrs.Rd
man/drop_sqs.Rd
man/error.Rd
man/fastCheckTreeMan.Rd
man/gb_extract.Rd
man/getAge.Rd
man/getBiprts.Rd
man/getCnnctdNds.Rd
man/getDcsd.Rd
man/getLvng.Rd
man/getNdAge.Rd
man/getNdKids.Rd
man/getNdLng.Rd
man/getNdPD.Rd
man/getNdPrdst.Rd
man/getNdPrids.Rd
man/getNdPtids.Rd
man/getNdSlt.Rd
man/getNdSstr.Rd
man/getNdsAge.Rd
man/getNdsFrmTxnyms.Rd
man/getNdsKids.Rd
man/getNdsLng.Rd
man/getNdsPD.Rd
man/getNdsPrdst.Rd
man/getNdsPrids.Rd
man/getNdsPtids.Rd
man/getNdsSlt.Rd
man/getNdsSstr.Rd
man/getOtgrp.Rd
man/getPath.Rd
man/getPrnt.Rd
man/getSpnAge.Rd
man/getSpnsAge.Rd
man/getSubtree.Rd
man/getUnqNds.Rd
man/get_clstr_slot.Rd
man/get_nsqs.Rd
man/get_ntaxa.Rd
man/get_sq_slot.Rd
man/get_stage_times.Rd
man/get_tx_slot.Rd
man/get_txids.Rd
man/hierarchic_download.Rd
man/info.Rd
man/isUltrmtrc.Rd
man/is_txid_in_clstr.Rd
man/is_txid_in_sq.Rd
man/list-to-TreeMen.Rd
man/list_clstrrec_slots.Rd
man/list_ncbi_ranks.Rd
man/list_seqrec_slots.Rd
man/list_taxrec_slots.Rd
man/loadTreeMan.Rd
man/mammals.Rd
man/mk_txid_in_sq_mtrx.Rd
man/multiPhylo-class.Rd
man/multiPhylo-to-TreeMen.Rd
man/ncbicache_load.Rd
man/ncbicache_save.Rd
man/obj_check.Rd
man/obj_load.Rd
man/obj_save.Rd
man/outfmt_get.Rd
man/parameters.Rd
man/parameters_load.Rd
man/parameters_reset.Rd
man/parameters_setup.Rd
man/parent_get.Rd
man/phylo-class.Rd
man/phylo-to-TreeMan.Rd
man/pinTips.Rd
man/plants.Rd
man/plot_phylota_pa.Rd
man/plot_phylota_treemap.Rd
man/progress_init.Rd
man/progress_read.Rd
man/progress_reset.Rd
man/progress_save.Rd
man/pstMnp.Rd
man/randTree.Rd
man/rank_get.Rd
man/rawseqrec_breakdown.Rd
man/readTree.Rd
man/readTrmn.Rd
man/read_phylota.Rd
man/reset.Rd
man/restart.Rd
man/rmClade.Rd
man/rmNdmtrx.Rd
man/rmNodes.Rd
man/rmOtherSlt.Rd
man/rmTips.Rd
man/run.Rd
man/safely_connect.Rd
man/saveTreeMan.Rd
man/searchTxnyms.Rd
man/search_and_cache.Rd
man/searchterm_gen.Rd
man/seeds_blast.Rd
man/seq_download.Rd
man/seqarc_gen.Rd
man/seqrec_augment.Rd
man/seqrec_convert.Rd
man/seqrec_gen.Rd
man/seqrec_get.Rd
man/setAge.Rd
man/setNdID.Rd
man/setNdOther.Rd
man/setNdSpn.Rd
man/setNdsID.Rd
man/setNdsOther.Rd
man/setNdsSpn.Rd
man/setPD.Rd
man/setTxnyms.Rd
man/setup.Rd
man/sids_check.Rd
man/sids_get.Rd
man/sids_load.Rd
man/sids_save.Rd
man/sqs_count.Rd
man/sqs_save.Rd
man/stage_args_check.Rd
man/stages_run.Rd
man/sturgeons.Rd
man/summary_phylota.Rd
man/tardigrades.Rd
man/tax_download.Rd
man/taxaResolve.Rd
man/taxdict_gen.Rd
man/taxise_run.Rd
man/taxtree_gen.Rd
man/tinamous.Rd
man/twoer.Rd
man/txids_get.Rd
man/txnds_count.Rd
man/ultrTree.Rd
man/unblncdTree.Rd
man/updateSlts.Rd
man/update_phylota.Rd
man/warn.Rd
man/writeTree.Rd
man/writeTrmn.Rd
man/write_sqs.Rd
man/yeasts.Rd
other/aedes_culex.R
other/birds.tre
other/dev.R
other/make_phylota_data.R
other/make_taxonomy_test_data.R
other/mammals.tre
other/plants.tre
other/spell_check.R
other/stages.png
other/unused.R
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
src/.gitignore
src/code.c
src/init.c
test.R
tests/test-all.R
tests/testthat/data/api/entrez_fetch_seqs.rda
tests/testthat/data/api/entrez_fetch_sid.rda
tests/testthat/data/api/entrez_search_sid.rda
tests/testthat/data/api/entrez_search_tax.rda
tests/testthat/data/api/xml_timeout.rda
tests/testthat/data/blast/README
tests/testthat/data/blast/blast_res.rda
tests/testthat/data/blast/testblstn
tests/testthat/data/blast/testdb.nhr
tests/testthat/data/blast/testdb.nin
tests/testthat/data/blast/testdb.nsq
tests/testthat/data/clstrarc.rda
tests/testthat/data/raw_seqrecs.rda
tests/testthat/data/raw_seqrecs2.rda
tests/testthat/data/raw_txrecs.rda
tests/testthat/data/sqrecs.rda
tests/testthat/data/taxonomy/txids_records.RData
tests/testthat/data/txdct.rda
tests/testthat/data/txrecs.rda
tests/testthat/test-all-class.R
tests/testthat/test-phylotar.R
tests/testthat/test-pipeline.R
tests/testthat/test-stage1-tools.R
tests/testthat/test-stage1.R
tests/testthat/test-stage2-tools.R
tests/testthat/test-stage2.R
tests/testthat/test-stage3-tools.R
tests/testthat/test-stage3.R
tests/testthat/test-stage4-tools.R
tests/testthat/test-stage4.R
tests/testthat/test-tools-api.R
tests/testthat/test-tools-blast.R
tests/testthat/test-tools-cache.R
tests/testthat/test-tools-entrez.R
tests/testthat/test-tools-log.R
tests/testthat/test-tools-pipeline.R
tests/testthat/test-tools-sqs.R
tests/testthat/test-tools-system.R
tests/testthat/test-tools-test.R
tests/testthat/test-tools-txdct.R
tests/testthat/test-user-calc.R
tests/testthat/test-user-drop.R
tests/testthat/test-user-get.R
tests/testthat/test-user-special.R
vignettes/phylotaR.R
vignettes/phylotaR.Rmd
vignettes/phylotaR.Rmd.orig
vignettes/precompile.R
vignettes/testing-1.png
