Package: phylotaR 1.3.0

Shixiang Wang

phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.

Authors:Shixiang Wang [aut, cre], Hannes Hettling [aut], Rutger Vos [aut], Alexander Zizka [aut], Dom Bennett [aut], Alexandre Antonelli [aut]

phylotaR_1.3.0.tar.gz
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phylotaR.pdf |phylotaR.html
phylotaR/json (API)

# Install phylotaR in R:
install.packages('phylotaR', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ropensci/phylotar/issues

Datasets:

On CRAN:

blastngenbankpeer-reviewedphylogeneticssequence-alignment

116 exports 23 stars 2.18 score 69 dependencies 8 downloads

Last updated 12 months agofrom:5e0bc06871ff7c85e75359e28a46ab750e6129b0 (via master)

Exports:addCladeaddNdmtrxaddTipblncdTreecalc_madcalc_wrdfrqcalcDstBLDcalcDstMtrxcalcDstRFcalcDstTrpcalcFrPrpcalcNdBlnccalcNdsBlnccalcOvrlpcalcPhyDvcalcPrtFrPrpcheckNdlstcheckTreeMenclusters_runclusters2_runcTreesdownload_rundrop_by_rankdrop_clstrsdrop_sqsfastCheckTreeManget_clstr_slotget_nsqsget_ntaxaget_sq_slotget_stage_timesget_tx_slotget_txidsgetAgegetBiprtsgetCnnctdNdsgetDcsdgetLvnggetNdAgegetNdKidsgetNdLnggetNdPDgetNdPrdstgetNdPridsgetNdPtidsgetNdsAgegetNdsFrmTxnymsgetNdsKidsgetNdsLnggetNdSltgetNdsPDgetNdsPrdstgetNdsPridsgetNdsPtidsgetNdsSltgetNdsSstrgetNdSstrgetOtgrpgetPathgetPrntgetSpnAgegetSpnsAgegetSubtreegetUnqNdsis_txid_in_clstris_txid_in_sqisUltrmtrclist_clstrrec_slotslist_ncbi_rankslist_seqrec_slotslist_taxrec_slotsloadTreeManoutfmt_getparametersparameters_resetpinTipsplot_phylota_paplot_phylota_treemapprintpstMnprandTreeread_phylotareadTreereadTrmnresetrestartrmCladermNdmtrxrmNodesrmOtherSltrmTipsrunsaveTreeMansearchTxnymssetAgesetNdIDsetNdOthersetNdsIDsetNdsOthersetNdSpnsetNdsSpnsetPDsetTxnymssetupshowstrsummarytaxaResolvetaxise_runtwoerultrTreeunblncdTreeupdateSltswrite_sqswriteTreewriteTrmn

Dependencies:apeaskpassassertthatBHbigmemorybigmemory.sriclicolorspacecommonmarkcpp11crayoncurlDBIdigestduckdbfansifarverfsggfittextggplot2gluegridtextgtablehttrigraphisobandjpegjsonlitelabelinglatticelifecyclemagrittrmarkdownMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigplyrpngR.methodsS3R.ooR.utilsR6RColorBrewerRcpprentrezrestezRJSONIOrlangscalesshadesstringistringrsystibbletreemapifyutf8uuidvctrsviridisLitewithrxfunXMLxml2

phylotaR Tutorial

Rendered fromphylotaR.Rmdusingknitr::rmarkdownon Jun 12 2024.

Last update: 2023-06-30
Started: 2018-03-27

Readme and manuals

Help Manual

Help pageTopics
Add clade to treeaddClade
Add node matrix to a treeaddNdmtrx
Add tip to a treeaddTip
aotusaotus
Download in batchesbatcher
birdsbirds
Cluster BLAST Resultsblast_clstr
Filter BLAST resultsblast_filter
Ensures NCBI BLAST tools are installedblast_setup
BLAST All vs Allblast_sqs
Load BLAST results from cacheblastcache_load
Save BLAST results to cacheblastcache_save
Generate a BLAST databaseblastdb_gen
Launch blastnblastn_run
Generate a balanced treeblncdTree
bromeliadsbromeliads
Delete a cachecache_rm
Set-up a cachecache_setup
Calculate MAD scorecalc_mad
Calculate word frequenciescalc_wrdfrq
Calculate the BLD between two treescalcDstBLD
Calculate the distance matrixcalcDstMtrx
Calculate the Robinson-Foulds distance between two treescalcDstRF
Calculate the triplet distance between two treescalcDstTrp
Calculate evolutionary distinctnesscalcFrPrp
Calculate the balance of a nodecalcNdBlnc
Calculate the balances of all nodescalcNdsBlnc
Calculate phylogenetic overlapcalcOvrlp
Calculate phylogenetic diversitycalcPhyDv
Calculate evolutionary distinctness for part of treecalcPrtFrPrp
Check if ndlst is correctcheckNdlst
Check if trees are correctcheckTreeMen
Get all node IDs that will be processedclade_select
Hierarchically cluster all sequences of a txidclstr_all
Cluster sequences directly associated with txidclstr_direct
Identify clusters from sequencesclstr_sqs
Cluster all sequences descending from a txidclstr_subtree
Cluster sets of clusters identified in cluster stageclstr2_calc
Generate cluster archive container classclstrarc_gen
Join two cluster archiveclstrarc_join
Cluster record archiveas.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 clustersclstrrec_gen
Cluster recordas.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 wdclstrs_calc
Join clusters for mergingclstrs_join
Merge joined clustersclstrs_merge
Renumber cluster IDsclstrs_renumber
Save clusters to cacheclstrs_save
Run the cluster stageclusters_run
Run the cluster2 stageclusters2_run
Run a command via terminal/command promptcmdln
cTreescTrees
cycadscycads
Get descendantsdescendants_get
Check an object returned from rentrez functiondownload_obj_check
Run download stagedownload_run
dragonfliesdragonflies
Reduce clusters to specific rankdrop_by_rank
Drop cluster records from phylota objectdrop_clstrs
Drop sequences in a clusterdrop_sqs
Write error message to logerror
Check if tree is correct, fast!fastCheckTreeMan
Extract elements from a raw GenBank recordgb_extract
Get slot data for each cluster recordget_clstr_slot
Count number of sequencesget_nsqs
Count number of unique taxaget_ntaxa
Get slot data for each sequenceget_sq_slot
Get run times for different stagesget_stage_times
Get slot data for each taxon recordget_tx_slot
Get taxonomic IDs by rankget_txids
Get age of treegetAge
Get the sets of labels for each bipartition in treegetBiprts
Get all nodes connected by given tipsgetCnnctdNds
Get extinct tips from a treegetDcsd
Get extant tips from a treegetLvng
Get agegetNdAge
Get children IDsgetNdKids
Get lineagegetNdLng
Get phylogenetic diversity of nodegetNdPD
Get pre-distancegetNdPrdst
Get pre-nodes to rootgetNdPrids
Get post-nodes to tipsgetNdPtids
Get ages for multiple nodesgetNdsAge
Get IDs for nodes represented txnymsgetNdsFrmTxnyms
Get children IDs for multiple nodesgetNdsKids
Get lineage for multiple nodesgetNdsLng
Get a node slotgetNdSlt
Get phylogenetic diversities of nodesgetNdsPD
Get pre-distancesgetNdsPrdst
Get pre-nodes for multiple nodesgetNdsPrids
Get post-nodes to tips for multiple nodesgetNdsPtids
Get a node slot for multiple nodesgetNdsSlt
Get sister idgetNdsSstr
Get sister idgetNdSstr
Get outgroupgetOtgrp
Get path between nodesgetPath
Get parentgetPrnt
Get age rangegetSpnAge
Get age ranges for multiple nodesgetSpnsAge
Get subtreegetSubtree
Get unique nodes represented by tipsgetUnqNds
Hierarchically get sequences for a txidhierarchic_download
Write info message to loginfo
Is txid in cluster?is_txid_in_clstr
Is txid in sequence?is_txid_in_sq
Is tree ultrametric?isUltrmtrc
List all ClstrRec slotslist_clstrrec_slots
List all NCBI Rankslist_ncbi_ranks
List all SeqRec slotslist_seqrec_slots
List all TaxRec slotslist_taxrec_slots
Convert list to a TreeMenlist-to-TreeMen
Load a TreeMan object in serialization formatloadTreeMan
mammalsmammals
Return matrix of txid in sequencemk_txid_in_sq_mtrx
multiPhylo classmultiPhylo multiPhylo-class
Convert multiPhylo to TreeMenmultiPhylo-to-TreeMen
Retrieve cached NCBI queryncbicache_load
Save NCBI query result to cachencbicache_save
Node-classas.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 existsobj_check
Load a named object from the cacheobj_load
Save a named object in the cacheobj_save
Determine 'outformat' formatoutfmt_get
Default parametersparameters
Load parameters from cacheparameters_load
Change parameters in a working directoryparameters_reset
Set Up Parametersparameters_setup
Get taxonomic parentparent_get
phylo classphylo phylo-class
Convert phylo to TreeManphylo-to-TreeMan
Phylota objectas.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 treepinTips
plantsplants
Plot presence/absence matrixplot_phylota_pa
Plot treemap of Phylota objectplot_phylota_treemap
Initialise progress list in cacheprogress_init
Read the progress from cacheprogress_read
Reset progressprogress_reset
Save current progressprogress_save
Update prinds and tindspstMnp
Generate a random treerandTree
Get rankrank_get
Breakdown a sequence record into its featuresrawseqrec_breakdown
Generate a Phylota object in Rread_phylota
Read a Newick treereadTree
Read a .trmn treereadTrmn
Reset a phylotaR pipeline runreset
Restart a phylotaR pipeline runrestart
Remove a clade from a treermClade
Remove node matrixrmNdmtrx
Remove nodes from a treermNodes
Remove a user-defined slotrmOtherSlt
Remove tips from a treermTips
Run phylotaR pipelinerun
Safely run rentrez functionsafely_connect
Save a TreeMan object in serialization formatsaveTreeMan
Run rentrez function and cache resultssearch_and_cache
Construct GenBank Search Termsearchterm_gen
Get node labels based on online taxonomic databasesearchTxnyms
BLAST seed sequencesseeds_blast
Download sequences for txidsseq_download
Generate sequence archiveseqarc_gen
Sequence record archiveas.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 listseqrec_augment
Convert raw Entrez gb text record to SeqRecsseqrec_convert
Generate sequence recordseqrec_gen
seqrec_getseqrec_get
Sequence recordas.character,SeqRec-method print,SeqRec-method SeqRec-class SeqRec-method show,SeqRec-method str,SeqRec-method summary,SeqRec-method
Set the age of a treesetAge
Set the ID of a nodesetNdID
Set a user defined slotsetNdOther
Set the IDs of multiple nodessetNdsID
Set a user defined slot for multiple nodessetNdsOther
Set the branch length of a specific nodesetNdSpn
Set the branch lengths of specific nodessetNdsSpn
Set the phylogenetic diversitysetPD
Set the txnym slots in a treesetTxnyms
Set-up parameterssetup
Check if sids existsids_check
Return random set of sequence IDssids_get
Load sids from cachesids_load
Save sids to cachesids_save
Count number of sequences for txidsqs_count
Save sequences to cachesqs_save
Check stage argumentsstage_args_check
Sequentially run each stagestages_run
sturgeonssturgeons
Summarise clusters in Phylota Tablesummary_phylota
tardigradestardigrades
Download taxonomic recordstax_download
Resolve taxonmic names onlinetaxaResolve
Generate taxonomic dictionarytaxdict_gen
Taxonomic record dictionaryas.character,TaxDict-method print,TaxDict-method show,TaxDict-method str,TaxDict-method summary,TaxDict-method TaxDict-class TaxDict-method
Run taxise stagetaxise_run
Taxonomic recordas.character,TaxRec-method print,TaxRec-method show,TaxRec-method str,TaxRec-method summary,TaxRec-method TaxRec-class TaxRec-method
Generate taxonomic treetaxtree_gen
tinamoustinamous
TreeMan-classas.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 phyloTreeMan-to-phylo
TreeMen-classa 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 multiPhyloTreeMen-to-multiPhylo
Generate a tree of two tipstwoer
Searches for descendant taxonomic IDstxids_get
Count number of descending taxonomic nodestxnds_count
Make tree ultrametricultrTree
Generate an unbalanced treeunblncdTree
Update slotsupdate_phylota
Update tree slots after manipulationupdateSlts
Write warning message to logwarn
Write out sequenceswrite_sqs
Write a Newick treewriteTree
Write a .trmn treewriteTrmn
yeastsyeasts