| Add clade to tree | addClade |
| Add node matrix to a tree | addNdmtrx |
| Add tip to a tree | addTip |
| aotus | aotus |
| Download in batches | batcher |
| birds | birds |
| Cluster BLAST Results | blast_clstr |
| Filter BLAST results | blast_filter |
| Ensures NCBI BLAST tools are installed | blast_setup |
| BLAST All vs All | blast_sqs |
| Load BLAST results from cache | blastcache_load |
| Save BLAST results to cache | blastcache_save |
| Generate a BLAST database | blastdb_gen |
| Launch blastn | blastn_run |
| Generate a balanced tree | blncdTree |
| bromeliads | bromeliads |
| Delete a cache | cache_rm |
| Set-up a cache | cache_setup |
| Calculate MAD score | calc_mad |
| Calculate word frequencies | calc_wrdfrq |
| Calculate the BLD between two trees | calcDstBLD |
| Calculate the distance matrix | calcDstMtrx |
| Calculate the Robinson-Foulds distance between two trees | calcDstRF |
| Calculate the triplet distance between two trees | calcDstTrp |
| Calculate evolutionary distinctness | calcFrPrp |
| Calculate the balance of a node | calcNdBlnc |
| Calculate the balances of all nodes | calcNdsBlnc |
| Calculate phylogenetic overlap | calcOvrlp |
| Calculate phylogenetic diversity | calcPhyDv |
| Calculate evolutionary distinctness for part of tree | calcPrtFrPrp |
| Check if ndlst is correct | checkNdlst |
| Check if trees are correct | checkTreeMen |
| Get all node IDs that will be processed | clade_select |
| Hierarchically cluster all sequences of a txid | clstr_all |
| Cluster sequences directly associated with txid | clstr_direct |
| Identify clusters from sequences | clstr_sqs |
| Cluster all sequences descending from a txid | clstr_subtree |
| Cluster sets of clusters identified in cluster stage | clstr2_calc |
| Generate cluster archive container class | clstrarc_gen |
| Join two cluster archive | clstrarc_join |
| Cluster record archive | as.character,ClstrArc-method ClstrArc-class ClstrArc-method print,ClstrArc-method show,ClstrArc-method str,ClstrArc-method summary,ClstrArc-method [,ClstrArc,character,missing,missing-method [[,ClstrArc,character-method |
| Generate list of clusters | clstrrec_gen |
| Cluster record | as.character,ClstrRec-method ClstrRec-class ClstrRec-method print,ClstrRec-method show,ClstrRec-method str,ClstrRec-method summary,ClstrRec-method |
| Calculate clusters for all sequences in wd | clstrs_calc |
| Join clusters for merging | clstrs_join |
| Merge joined clusters | clstrs_merge |
| Renumber cluster IDs | clstrs_renumber |
| Save clusters to cache | clstrs_save |
| Run the cluster stage | clusters_run |
| Run the cluster2 stage | clusters2_run |
| Run a command via terminal/command prompt | cmdln |
| cTrees | cTrees |
| cycads | cycads |
| Get descendants | descendants_get |
| Check an object returned from rentrez function | download_obj_check |
| Run download stage | download_run |
| dragonflies | dragonflies |
| Reduce clusters to specific rank | drop_by_rank |
| Drop cluster records from phylota object | drop_clstrs |
| Drop sequences in a cluster | drop_sqs |
| Write error message to log | error |
| Check if tree is correct, fast! | fastCheckTreeMan |
| Extract elements from a raw GenBank record | gb_extract |
| Get slot data for each cluster record | get_clstr_slot |
| Count number of sequences | get_nsqs |
| Count number of unique taxa | get_ntaxa |
| Get slot data for each sequence | get_sq_slot |
| Get run times for different stages | get_stage_times |
| Get slot data for each taxon record | get_tx_slot |
| Get taxonomic IDs by rank | get_txids |
| Get age of tree | getAge |
| Get the sets of labels for each bipartition in tree | getBiprts |
| Get all nodes connected by given tips | getCnnctdNds |
| Get extinct tips from a tree | getDcsd |
| Get extant tips from a tree | getLvng |
| Get age | getNdAge |
| Get children IDs | getNdKids |
| Get lineage | getNdLng |
| Get phylogenetic diversity of node | getNdPD |
| Get pre-distance | getNdPrdst |
| Get pre-nodes to root | getNdPrids |
| Get post-nodes to tips | getNdPtids |
| Get ages for multiple nodes | getNdsAge |
| Get IDs for nodes represented txnyms | getNdsFrmTxnyms |
| Get children IDs for multiple nodes | getNdsKids |
| Get lineage for multiple nodes | getNdsLng |
| Get a node slot | getNdSlt |
| Get phylogenetic diversities of nodes | getNdsPD |
| Get pre-distances | getNdsPrdst |
| Get pre-nodes for multiple nodes | getNdsPrids |
| Get post-nodes to tips for multiple nodes | getNdsPtids |
| Get a node slot for multiple nodes | getNdsSlt |
| Get sister id | getNdsSstr |
| Get sister id | getNdSstr |
| Get outgroup | getOtgrp |
| Get path between nodes | getPath |
| Get parent | getPrnt |
| Get age range | getSpnAge |
| Get age ranges for multiple nodes | getSpnsAge |
| Get subtree | getSubtree |
| Get unique nodes represented by tips | getUnqNds |
| Hierarchically get sequences for a txid | hierarchic_download |
| Write info message to log | info |
| Is txid in cluster? | is_txid_in_clstr |
| Is txid in sequence? | is_txid_in_sq |
| Is tree ultrametric? | isUltrmtrc |
| List all ClstrRec slots | list_clstrrec_slots |
| List all NCBI Ranks | list_ncbi_ranks |
| List all SeqRec slots | list_seqrec_slots |
| List all TaxRec slots | list_taxrec_slots |
| Convert list to a TreeMen | list-to-TreeMen |
| Load a TreeMan object in serialization format | loadTreeMan |
| mammals | mammals |
| Return matrix of txid in sequence | mk_txid_in_sq_mtrx |
| multiPhylo class | multiPhylo multiPhylo-class |
| Convert multiPhylo to TreeMen | multiPhylo-to-TreeMen |
| Retrieve cached NCBI query | ncbicache_load |
| Save NCBI query result to cache | ncbicache_save |
| Node-class | as.character,Node-method Node-class Node-method print,Node-method show,Node-method summary,Node-method [,Node,character,missing,missing-method |
| Check if an object exists | obj_check |
| Load a named object from the cache | obj_load |
| Save a named object in the cache | obj_save |
| Determine 'outformat' format | outfmt_get |
| Default parameters | parameters |
| Load parameters from cache | parameters_load |
| Change parameters in a working directory | parameters_reset |
| Set Up Parameters | parameters_setup |
| Get taxonomic parent | parent_get |
| phylo class | phylo phylo-class |
| Convert phylo to TreeMan | phylo-to-TreeMan |
| Phylota object | as.character,Phylota-method Phylota-class Phylota-method print,Phylota-method show,Phylota-method str,Phylota-method summary,Phylota-method [[,Phylota,character-method |
| Pin tips to a tree | pinTips |
| plants | plants |
| Plot presence/absence matrix | plot_phylota_pa |
| Plot treemap of Phylota object | plot_phylota_treemap |
| Initialise progress list in cache | progress_init |
| Read the progress from cache | progress_read |
| Reset progress | progress_reset |
| Save current progress | progress_save |
| Update prinds and tinds | pstMnp |
| Generate a random tree | randTree |
| Get rank | rank_get |
| Breakdown a sequence record into its features | rawseqrec_breakdown |
| Generate a Phylota object in R | read_phylota |
| Read a Newick tree | readTree |
| Read a .trmn tree | readTrmn |
| Reset a phylotaR pipeline run | reset |
| Restart a phylotaR pipeline run | restart |
| Remove a clade from a tree | rmClade |
| Remove node matrix | rmNdmtrx |
| Remove nodes from a tree | rmNodes |
| Remove a user-defined slot | rmOtherSlt |
| Remove tips from a tree | rmTips |
| Run phylotaR pipeline | run |
| Safely run rentrez function | safely_connect |
| Save a TreeMan object in serialization format | saveTreeMan |
| Run rentrez function and cache results | search_and_cache |
| Construct GenBank Search Term | searchterm_gen |
| Get node labels based on online taxonomic database | searchTxnyms |
| BLAST seed sequences | seeds_blast |
| Download sequences for txids | seq_download |
| Generate sequence archive | seqarc_gen |
| Sequence record archive | as.character,SeqArc-method print,SeqArc-method SeqArc-class SeqArc-method show,SeqArc-method str,SeqArc-method summary,SeqArc-method [,SeqArc,character,missing,missing-method [[,SeqArc,character-method |
| Augment sequence records list | seqrec_augment |
| Convert raw Entrez gb text record to SeqRecs | seqrec_convert |
| Generate sequence record | seqrec_gen |
| seqrec_get | seqrec_get |
| Sequence record | as.character,SeqRec-method print,SeqRec-method SeqRec-class SeqRec-method show,SeqRec-method str,SeqRec-method summary,SeqRec-method |
| Set the age of a tree | setAge |
| Set the ID of a node | setNdID |
| Set a user defined slot | setNdOther |
| Set the IDs of multiple nodes | setNdsID |
| Set a user defined slot for multiple nodes | setNdsOther |
| Set the branch length of a specific node | setNdSpn |
| Set the branch lengths of specific nodes | setNdsSpn |
| Set the phylogenetic diversity | setPD |
| Set the txnym slots in a tree | setTxnyms |
| Set-up parameters | setup |
| Check if sids exist | sids_check |
| Return random set of sequence IDs | sids_get |
| Load sids from cache | sids_load |
| Save sids to cache | sids_save |
| Count number of sequences for txid | sqs_count |
| Save sequences to cache | sqs_save |
| Check stage arguments | stage_args_check |
| Sequentially run each stage | stages_run |
| sturgeons | sturgeons |
| Summarise clusters in Phylota Table | summary_phylota |
| tardigrades | tardigrades |
| Download taxonomic records | tax_download |
| Resolve taxonmic names online | taxaResolve |
| Generate taxonomic dictionary | taxdict_gen |
| Taxonomic record dictionary | as.character,TaxDict-method print,TaxDict-method show,TaxDict-method str,TaxDict-method summary,TaxDict-method TaxDict-class TaxDict-method |
| Run taxise stage | taxise_run |
| Taxonomic record | as.character,TaxRec-method print,TaxRec-method show,TaxRec-method str,TaxRec-method summary,TaxRec-method TaxRec-class TaxRec-method |
| Generate taxonomic tree | taxtree_gen |
| tinamous | tinamous |
| TreeMan-class | as.character,TreeMan-method cTrees,TreeMan-method print,TreeMan-method show,TreeMan-method str,TreeMan-method summary,TreeMan-method TreeMan-class TreeMan-method [,TreeMan,character,missing,missing-method [[,TreeMan,character-method |
| Convert TreeMan to phylo | TreeMan-to-phylo |
| TreeMen-class | a as.character,TreeMen-method cTrees,TreeMen-method Extract from list of print,TreeMen-method show,TreeMen-method slots str,TreeMen-method summary,TreeMen-method TreeMen-class TreeMen-method trees [,TreeMen,character,missing,missing-method [[,TreeMen,ANY-method |
| Convert TreeMen to multiPhylo | TreeMen-to-multiPhylo |
| Generate a tree of two tips | twoer |
| Searches for descendant taxonomic IDs | txids_get |
| Count number of descending taxonomic nodes | txnds_count |
| Make tree ultrametric | ultrTree |
| Generate an unbalanced tree | unblncdTree |
| Update slots | update_phylota |
| Update tree slots after manipulation | updateSlts |
| Write warning message to log | warn |
| Write out sequences | write_sqs |
| Write a Newick tree | writeTree |
| Write a .trmn tree | writeTrmn |
| yeasts | yeasts |
