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