API for ropensci/phylotaR
Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
| Global functions | |
|---|---|
| .cMenToAny | Source code |
| .cMenToMan | Source code |
| .cMenToMen | Source code |
| .cTreeObjs | Source code |
| .cnstrctTree | Source code |
| .findClade | Source code |
| .getNdKidsFrmLst | Source code |
| .getNdPDFrmLst | Source code |
| .getNdPrdstsFrmLst | Source code |
| .getNdPridsFrmLst | Source code |
| .getNdPtidsFrmLst | Source code |
| .getNdSstrFrmLst | Source code |
| .getNdmtrxFrmLst | Source code |
| .getNdsKidsFrmLst | Source code |
| .getNdsKidsFrmMtrx | Source code |
| .getNdsPDFrmLst | Source code |
| .getNdsPDFrmMtrx | Source code |
| .getNdsPrdstsFrmLst | Source code |
| .getNdsPrdstsFrmMtrx | Source code |
| .getNdsPridsFrmLst | Source code |
| .getNdsPridsFrmMtrx | Source code |
| .getNdsPtidsFrmLst | Source code |
| .getNdsPtidsFrmMtrx | Source code |
| .getPrinds | Source code |
| .getSltSpns | Source code |
| .getTinds | Source code |
| .getTreeAgeFrmLst | Source code |
| .getTreeAgeFrmMtrx | Source code |
| .livingOrDesceased | Source code |
| .log | Source code |
| .newNd | Source code |
| .preCtest | Source code |
| .readTree | Source code |
| .readTrmn | Source code |
| .safeFromJSON | Source code |
| .stgMsg | Source code |
| .untar | Source code |
| .writeTree | Source code |
| ClstrArc-class | Man page |
| ClstrArc-method | Man page |
| ClstrRec-class | Man page |
| ClstrRec-method | Man page |
| Extract | Man page |
| Node-class | Man page |
| Node-method | Man page |
| Phylota-class | Man page |
| Phylota-method | Man page |
| SeqArc-class | Man page |
| SeqArc-method | Man page |
| SeqRec-class | Man page |
| SeqRec-method | Man page |
| TaxDict-class | Man page |
| TaxDict-method | Man page |
| TaxRec-class | Man page |
| TaxRec-method | Man page |
| TreeMan-class | Man page |
| TreeMan-method | Man page |
| TreeMan-to-phylo | Man page |
| TreeMen-class | Man page |
| TreeMen-method | Man page |
| TreeMen-to-multiPhylo | Man page |
| [,ClstrArc,character,missing,missing-method | Man page |
| [,Node,character,missing,missing-method | Man page |
| [,SeqArc,character,missing,missing-method | Man page |
| [,TreeMan,character,missing,missing-method | Man page |
| [,TreeMen,character,missing,missing-method | Man page |
| [[,ClstrArc,character-method | Man page |
| [[,Phylota,character-method | Man page |
| [[,SeqArc,character-method | Man page |
| [[,TreeMan,character-method | Man page |
| [[,TreeMen,ANY-method | Man page |
| a | Man page |
| addClade | Man page Source code |
| addNdmtrx | Man page Source code |
| addTip | Man page Source code |
| aotus | Man page |
| as.character,ClstrArc-method | Man page |
| as.character,ClstrRec-method | Man page |
| as.character,Node-method | Man page |
| as.character,Phylota-method | Man page |
| as.character,SeqArc-method | Man page |
| as.character,SeqRec-method | Man page |
| as.character,TaxDict-method | Man page |
| as.character,TaxRec-method | Man page |
| as.character,TreeMan-method | Man page |
| as.character,TreeMen-method | Man page |
| batcher | Man page Source code |
| birds | Man page |
| blast_clstr | Man page Source code |
| blast_filter | Man page Source code |
| blast_setup | Man page Source code |
| blast_sqs | Man page Source code |
| blastcache_load | Man page Source code |
| blastcache_save | Man page Source code |
| blastdb_gen | Man page Source code |
| blastn_run | Man page Source code |
| blncdTree | Man page Source code |
| bromeliads | Man page |
| cTrees | Man page |
| cTrees,TreeMan-method | Man page |
| cTrees,TreeMen-method | Man page |
| cache_rm | Man page Source code |
| cache_setup | Man page Source code |
| calcDstBLD | Man page Source code |
| calcDstMtrx | Man page Source code |
| calcDstRF | Man page Source code |
| calcDstTrp | Man page Source code |
| calcFrPrp | Man page Source code |
| calcNdBlnc | Man page Source code |
| calcNdsBlnc | Man page Source code |
| calcOvrlp | Man page Source code |
| calcPhyDv | Man page Source code |
| calcPrtFrPrp | Man page Source code |
| calc_mad | Man page Source code |
| calc_wrdfrq | Man page Source code |
| checkNdlst | Man page Source code |
| checkTreeMen | Man page Source code |
| clade_select | Man page Source code |
| cleanup | Source code |
| clstr2_calc | Man page Source code |
| clstr_all | Man page Source code |
| clstr_direct | Man page Source code |
| clstr_sqs | Man page Source code |
| clstr_subtree | Man page Source code |
| clstrarc_check | Source code |
| clstrarc_gen | Man page Source code |
| clstrarc_join | Man page Source code |
| clstrrec_gen | Man page Source code |
| clstrs_calc | Man page Source code |
| clstrs_join | Man page Source code |
| clstrs_merge | Man page Source code |
| clstrs_renumber | Man page Source code |
| clstrs_save | Man page Source code |
| clusters2_run | Man page Source code |
| clusters_run | Man page Source code |
| cmdln | Man page Source code |
| cmdln_blastcheck | Source code |
| cycads | Man page |
| datadir_get | Source code |
| descendants_get | Man page Source code |
| download_obj_check | Man page Source code |
| download_run | Man page Source code |
| dragonflies | Man page |
| drop_by_rank | Man page Source code |
| drop_clstrs | Man page Source code |
| drop_sqs | Man page Source code |
| error | Man page Source code |
| fastCheckTreeMan | Man page Source code |
| from | Man page |
| gb_extract | Man page Source code |
| getAge | Man page Source code |
| getBiprts | Man page Source code |
| getCnnctdNds | Man page Source code |
| getDcsd | Man page Source code |
| getLvng | Man page Source code |
| getNdAge | Man page Source code |
| getNdKids | Man page Source code |
| getNdLng | Man page Source code |
| getNdPD | Man page Source code |
| getNdPrdst | Man page Source code |
| getNdPrids | Man page Source code |
| getNdPtids | Man page Source code |
| getNdSlt | Man page Source code |
| getNdSstr | Man page Source code |
| getNdsAge | Man page Source code |
| getNdsFrmTxnyms | Man page Source code |
| getNdsKids | Man page Source code |
| getNdsLng | Man page Source code |
| getNdsPD | Man page Source code |
| getNdsPrdst | Man page Source code |
| getNdsPrids | Man page Source code |
| getNdsPtids | Man page Source code |
| getNdsSlt | Man page Source code |
| getNdsSstr | Man page Source code |
| getOtgrp | Man page Source code |
| getPath | Man page Source code |
| getPrnt | Man page Source code |
| getSpnAge | Man page Source code |
| getSpnsAge | Man page Source code |
| getSubtree | Man page Source code |
| getUnqNds | Man page Source code |
| get_clstr_slot | Man page Source code |
| get_nsqs | Man page Source code |
| get_ntaxa | Man page Source code |
| get_sq_slot | Man page Source code |
| get_stage_times | Man page Source code |
| get_tx_slot | Man page Source code |
| get_txids | Man page Source code |
| hierarchic_download | Man page Source code |
| info | Man page Source code |
| isUltrmtrc | Man page Source code |
| is_txid_in_clstr | Man page Source code |
| is_txid_in_sq | Man page Source code |
| list | Man page |
| list-to-TreeMen | Man page |
| list_clstrrec_slots | Man page Source code |
| list_ncbi_ranks | Man page Source code |
| list_seqrec_slots | Man page Source code |
| list_taxrec_slots | Man page Source code |
| loadTreeMan | Man page Source code |
| mammals | Man page |
| mk_txid_in_sq_mtrx | Man page Source code |
| multiPhylo | Man page |
| multiPhylo-class | Man page |
| multiPhylo-to-TreeMen | Man page |
| ncbicache_load | Man page Source code |
| ncbicache_save | Man page Source code |
| obj_check | Man page Source code |
| obj_load | Man page Source code |
| obj_save | Man page Source code |
| of | Man page |
| outfmt_get | Man page Source code |
| outsider_call | Source code |
| parameters | Man page Source code |
| parameters_load | Man page Source code |
| parameters_reset | Man page Source code |
| parameters_setup | Man page Source code |
| parent_get | Man page Source code |
| parent_recs_get | Source code |
| phylo | Man page |
| phylo-class | Man page |
| phylo-to-TreeMan | Man page |
| phylota_check | Source code |
| pinTips | Man page Source code |
| plants | Man page |
| plot_phylota_pa | Man page Source code |
| plot_phylota_treemap | Man page Source code |
| print,ClstrArc-method | Man page |
| print,ClstrRec-method | Man page |
| print,Node-method | Man page |
| print,Phylota-method | Man page |
| print,SeqArc-method | Man page |
| print,SeqRec-method | Man page |
| print,TaxDict-method | Man page |
| print,TaxRec-method | Man page |
| print,TreeMan-method | Man page |
| print,TreeMen-method | Man page |
| progress_init | Man page Source code |
| progress_read | Man page Source code |
| progress_reset | Man page Source code |
| progress_save | Man page Source code |
| pstMnp | Man page Source code |
| randTree | Man page Source code |
| random_phylota | Source code |
| rank_get | Man page Source code |
| rawseqrec_breakdown | Man page Source code |
| readTree | Man page Source code |
| readTrmn | Man page Source code |
| read_phylota | Man page Source code |
| reset | Man page Source code |
| restart | Man page Source code |
| rmClade | Man page Source code |
| rmNdmtrx | Man page Source code |
| rmNodes | Man page Source code |
| rmOtherSlt | Man page Source code |
| rmTips | Man page Source code |
| run | Man page Source code |
| safely_connect | Man page Source code |
| saveTreeMan | Man page Source code |
| searchTxnyms | Man page Source code |
| search_and_cache | Man page Source code |
| searchterm_gen | Man page Source code |
| seeds_blast | Man page Source code |
| seq_download | Man page Source code |
| seqarc_check | Source code |
| seqarc_gen | Man page Source code |
| seqrec_augment | Man page Source code |
| seqrec_check | Source code |
| seqrec_convert | Man page Source code |
| seqrec_gen | Man page Source code |
| seqrec_get | Man page Source code |
| setAge | Man page Source code |
| setNdID | Man page Source code |
| setNdOther | Man page Source code |
| setNdSpn | Man page Source code |
| setNdsID | Man page Source code |
| setNdsOther | Man page Source code |
| setNdsSpn | Man page Source code |
| setPD | Man page Source code |
| setTxnyms | Man page Source code |
| setup | Man page Source code |
| show,ClstrArc-method | Man page |
| show,ClstrRec-method | Man page |
| show,Node-method | Man page |
| show,Phylota-method | Man page |
| show,SeqArc-method | Man page |
| show,SeqRec-method | Man page |
| show,TaxDict-method | Man page |
| show,TaxRec-method | Man page |
| show,TreeMan-method | Man page |
| show,TreeMen-method | Man page |
| sids_check | Man page Source code |
| sids_get | Man page Source code |
| sids_load | Man page Source code |
| sids_save | Man page Source code |
| slots | Man page |
| sqs_count | Man page Source code |
| sqs_save | Man page Source code |
| stage_args_check | Man page Source code |
| stages_run | Man page Source code |
| str,ClstrArc-method | Man page |
| str,ClstrRec-method | Man page |
| str,Phylota-method | Man page |
| str,SeqArc-method | Man page |
| str,SeqRec-method | Man page |
| str,TaxDict-method | Man page |
| str,TaxRec-method | Man page |
| str,TreeMan-method | Man page |
| str,TreeMen-method | Man page |
| sturgeons | Man page |
| summary,ClstrArc-method | Man page |
| summary,ClstrRec-method | Man page |
| summary,Node-method | Man page |
| summary,Phylota-method | Man page |
| summary,SeqArc-method | Man page |
| summary,SeqRec-method | Man page |
| summary,TaxDict-method | Man page |
| summary,TaxRec-method | Man page |
| summary,TreeMan-method | Man page |
| summary,TreeMen-method | Man page |
| summary_phylota | Man page Source code |
| sys_exec | Source code |
| tardigrades | Man page |
| tax_download | Man page Source code |
| taxaResolve | Man page Source code |
| taxdict_check | Source code |
| taxdict_gen | Man page Source code |
| taxise_run | Man page Source code |
| taxrec_check | Source code |
| taxtree_gen | Man page Source code |
| testsqs_gen | Source code |
| tinamous | Man page |
| trees | Man page |
| twoer | Man page Source code |
| txids_get | Man page Source code |
| txnds_count | Man page Source code |
| ultrTree | Man page Source code |
| unblncdTree | Man page Source code |
| updateSlts | Man page Source code |
| update_phylota | Man page Source code |
| warn | Man page Source code |
| writeTree | Man page Source code |
| writeTrmn | Man page Source code |
| write_sqs | Man page Source code |
| yeasts | Man page |
