PhyloNetworks.jl
PhyloNetworks is a Julia package for the manipulation, visualization, inference of phylogenetic networks, and their use for trait evolution.
How to get help
- the package wiki has a step-by-step tutorial, done for the MBL workshop (last revised 2022), with background on networks and explanations.
- tutorial for comparative methods, including network calibration (2023 workshop)
- the google group has answers to common questions.
- the Manual below has a quick tutorial (navigation on the left).
- the Library and and Index further below has the full list of documented functions.
References
See their bibtex format.
for the package:
- Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017). PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution 34(12):3292–3298. doi:10.1093/molbev/msx235
for trait evolution:
- Teo, Rose, Bastide & Ané (2022). Accounting for intraspecific variation in continuous trait evolution on a reticulate phylogeny. bioRxiv
- Karimi, Grover, Gallagher, Wendel, Ané & Baum (2020). Reticulate evolution helps explain apparent homoplasy in floral biology and pollination in baobabs (Adansonia; Bombacoideae; Malvaceae). Systematic Biology, 69(3):462-478. doi:10.1093/sysbio/syz073.
- Bastide, Solís-Lemus, Kriebel, Sparks, Ané (2018). Phylogenetic Comparative Methods for Phylogenetic Networks with Reticulations. Systematic Biology, 67(5):800–820. doi:10.1093/sysbio/syy033.
for network inference:
- Claudia Solís-Lemus and Cécile Ané (2016). Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting. PLoS Genet 12(3):e1005896. doi:10.1371/journal.pgen.1005896
Manual
- Installation
- Network manipulation
- Input for SNaQ
- TICR pipeline
- Getting a Network
- Comparing and manipulating networks
- Candidate Networks
- Extract Expected CFs
- Bootstrap
- Multiple alleles per species
- Continuous Trait Evolution
- Parsimony on networks
- Neighbor joining
Library
Index
Functions
Base.getindex
PhyloNetworks.Q
PhyloNetworks.ancestralStateReconstruction
PhyloNetworks.biconnectedComponents
PhyloNetworks.blobDecomposition
PhyloNetworks.bootsnaq
PhyloNetworks.calibrateFromPairwiseDistances!
PhyloNetworks.checkroot!
PhyloNetworks.cladewiseorder!
PhyloNetworks.countquartetsintrees
PhyloNetworks.deleteHybridThreshold!
PhyloNetworks.deleteaboveLSA!
PhyloNetworks.deleteleaf!
PhyloNetworks.descendenceMatrix
PhyloNetworks.directEdges!
PhyloNetworks.displayedNetworkAt!
PhyloNetworks.displayedTrees
PhyloNetworks.empiricalDNAfrequencies
PhyloNetworks.expectations
PhyloNetworks.expectationsPlot
PhyloNetworks.fitdiscrete
PhyloNetworks.fittedQuartetCF
PhyloNetworks.getNodeAges
PhyloNetworks.getShiftEdgeNumber
PhyloNetworks.getShiftValue
PhyloNetworks.getchild
PhyloNetworks.getlabels
PhyloNetworks.getparent
PhyloNetworks.getpartneredge
PhyloNetworks.getroot
PhyloNetworks.hardwiredCluster
PhyloNetworks.hardwiredClusterDistance
PhyloNetworks.hardwiredClusters
PhyloNetworks.hassinglechild
PhyloNetworks.hybridBootstrapSupport
PhyloNetworks.hybridDetection
PhyloNetworks.hybridatnode!
PhyloNetworks.hybridlambdaformat
PhyloNetworks.isparentof
PhyloNetworks.isrootof
PhyloNetworks.lambda_estim
PhyloNetworks.majorTree
PhyloNetworks.mapAllelesCFtable
PhyloNetworks.maxParsimonyNet
PhyloNetworks.minorTreeAt
PhyloNetworks.mu_phylo
PhyloNetworks.nj
PhyloNetworks.nni!
PhyloNetworks.nparams
PhyloNetworks.nstates
PhyloNetworks.pairwiseTaxonDistanceMatrix
PhyloNetworks.parsimonyGF
PhyloNetworks.parsimonySoftwired
PhyloNetworks.phylolm
PhyloNetworks.predint
PhyloNetworks.predintPlot
PhyloNetworks.preorder!
PhyloNetworks.printEdges
PhyloNetworks.printNodes
PhyloNetworks.randomTrait
PhyloNetworks.randomTrait!
PhyloNetworks.readBootstrapTrees
PhyloNetworks.readInputTrees
PhyloNetworks.readMultiTopology
PhyloNetworks.readSnaqNetwork
PhyloNetworks.readTableCF
PhyloNetworks.readTableCF!
PhyloNetworks.readTopology
PhyloNetworks.readTopologyLevel1
PhyloNetworks.readTrees2CF
PhyloNetworks.readfastatodna
PhyloNetworks.readnexus_treeblock
PhyloNetworks.regressorHybrid
PhyloNetworks.regressorShift
PhyloNetworks.removedegree2nodes!
PhyloNetworks.rootatnode!
PhyloNetworks.rootonedge!
PhyloNetworks.rotate!
PhyloNetworks.setGamma!
PhyloNetworks.setLength!
PhyloNetworks.sharedPathMatrix
PhyloNetworks.shiftHybrid
PhyloNetworks.shrink2cycles!
PhyloNetworks.shrink3cycles!
PhyloNetworks.sigma2_phylo
PhyloNetworks.sigma2_within
PhyloNetworks.simulate
PhyloNetworks.snaq!
PhyloNetworks.sorttaxa!
PhyloNetworks.stationary
PhyloNetworks.summarizeDataCF
PhyloNetworks.summarizeHFdf
PhyloNetworks.tipLabels
PhyloNetworks.topologyMaxQPseudolik!
PhyloNetworks.topologyQPseudolik!
PhyloNetworks.treeEdgesBootstrap
PhyloNetworks.treeedgecomponents
PhyloNetworks.undirectedOtherNetworks
PhyloNetworks.vcv
PhyloNetworks.writeMultiTopology
PhyloNetworks.writeSubTree!
PhyloNetworks.writeTableCF
PhyloNetworks.writeTopology
Base.getindex
Base.getindex
PhyloNetworks.P
PhyloNetworks.P!
PhyloNetworks.addAlternativeHybridizations!
PhyloNetworks.addHybridBetweenClades!
PhyloNetworks.addhybridedge!
PhyloNetworks.addhybridedge!
PhyloNetworks.addhybridedgeLiNC!
PhyloNetworks.addindividuals!
PhyloNetworks.addleaf!
PhyloNetworks.adjacentedges
PhyloNetworks.afterOptBL!
PhyloNetworks.afterOptBLAll!
PhyloNetworks.afterOptBLRepeat!
PhyloNetworks.allowrootbelow!
PhyloNetworks.allowrootbelow!
PhyloNetworks.anova
PhyloNetworks.assignhybridnames!
PhyloNetworks.biconnectedcomponent_entrynodes
PhyloNetworks.biconnectedcomponent_exitnodes
PhyloNetworks.blobInfo
PhyloNetworks.breakedge!
PhyloNetworks.calculateObsCFAll!
PhyloNetworks.checkMapDF
PhyloNetworks.checkNumHybEdges!
PhyloNetworks.check_matchtaxonnames!
PhyloNetworks.check_nonmissing_nonnegative_edgelengths
PhyloNetworks.checknetwork_LiNC!
PhyloNetworks.checkspeciesnetwork!
PhyloNetworks.cleantaxonname
PhyloNetworks.constraintviolated
PhyloNetworks.defaultsubstitutionmodel
PhyloNetworks.deleteEdge!
PhyloNetworks.deleteLeaf!
PhyloNetworks.deleteNode!
PhyloNetworks.deletehybridedge!
PhyloNetworks.deletehybridedgeLiNC!
PhyloNetworks.descendants
PhyloNetworks.directionalconflict
PhyloNetworks.discrete_backwardlikelihood_trait!
PhyloNetworks.discrete_corelikelihood!
PhyloNetworks.discrete_corelikelihood_trait!
PhyloNetworks.displayedNetworks!
PhyloNetworks.edgerelation
PhyloNetworks.fliphybrid!
PhyloNetworks.fliphybrid!
PhyloNetworks.fliphybridedgeLiNC!
PhyloNetworks.fuseedgesat!
PhyloNetworks.gammaZero!
PhyloNetworks.getDataValue!
PhyloNetworks.getGammas
PhyloNetworks.getHeights
PhyloNetworks.getNeighborsTarget
PhyloNetworks.getTipSubmatrix
PhyloNetworks.getlengths
PhyloNetworks.getparameters
PhyloNetworks.getparamindex
PhyloNetworks.hardwiredClusterDistance_unrooted
PhyloNetworks.hashybridladder
PhyloNetworks.hybrid3cycle
PhyloNetworks.hybridEdges
PhyloNetworks.hybridEdges
PhyloNetworks.hybridatnode
PhyloNetworks.inheritanceWeight
PhyloNetworks.initializeWeightsFromLeaves!
PhyloNetworks.initializeWeightsFromLeavesSoftwired!
PhyloNetworks.isconnected
PhyloNetworks.isdescendant
PhyloNetworks.isdescendant_undirected
PhyloNetworks.ladderpartition
PhyloNetworks.lambda
PhyloNetworks.lambda!
PhyloNetworks.learnlabels
PhyloNetworks.leaststableancestor
PhyloNetworks.majoredgelength
PhyloNetworks.majoredgematrix
PhyloNetworks.makemissing!
PhyloNetworks.mapAllelesCFtable!
PhyloNetworks.mapindividuals
PhyloNetworks.maxParsimonyNetRun1
PhyloNetworks.maxParsimonyNetRun1!
PhyloNetworks.minorreticulationgamma
PhyloNetworks.minorreticulationlength
PhyloNetworks.minorreticulationmatrix
PhyloNetworks.moveHybrid!
PhyloNetworks.moveTargetUpdate!
PhyloNetworks.moveroot!
PhyloNetworks.nameinternalnodes!
PhyloNetworks.nchoose1234
PhyloNetworks.nj!
PhyloNetworks.nni_LiNC!
PhyloNetworks.nnimax
PhyloNetworks.norootbelow!
PhyloNetworks.optBL!
PhyloNetworks.optTopLevel!
PhyloNetworks.optTopRun1!
PhyloNetworks.optTopRuns!
PhyloNetworks.optimizeallgammas_LiNC!
PhyloNetworks.optimizealllengths_LiNC!
PhyloNetworks.optimizegamma_LiNC!
PhyloNetworks.optimizelength_LiNC!
PhyloNetworks.optimizelocalBL_LiNC!
PhyloNetworks.optimizelocalgammas_LiNC!
PhyloNetworks.optimizestructure!
PhyloNetworks.pairwiseTaxonDistanceGrad
PhyloNetworks.parseEdgeData!
PhyloNetworks.parseHybridNode!
PhyloNetworks.parseRemainingSubtree!
PhyloNetworks.parseTreeNode!
PhyloNetworks.parsimonyBottomUpFitch!
PhyloNetworks.parsimonyBottomUpGF!
PhyloNetworks.parsimonyBottomUpSoftwired!
PhyloNetworks.parsimonyDiscreteFitch
PhyloNetworks.parsimonySummaryFitch
PhyloNetworks.parsimonyTopDownFitch!
PhyloNetworks.phyLiNC
PhyloNetworks.phyLiNC!
PhyloNetworks.phyLiNCone!
PhyloNetworks.posterior_loghybridweight
PhyloNetworks.posterior_logtreeweight
PhyloNetworks.problem4cycle
PhyloNetworks.proposedTop!
PhyloNetworks.quartetdata_columnnames
PhyloNetworks.quartetrank
PhyloNetworks.readCSVtoArray
PhyloNetworks.readFastaToArray
PhyloNetworks.readInputData
PhyloNetworks.readSubtree!
PhyloNetworks.readnexus_assigngammas!
PhyloNetworks.readnexus_extractgamma
PhyloNetworks.readnexus_translatetable
PhyloNetworks.readnexuscomment
PhyloNetworks.readnodename
PhyloNetworks.recursionPostOrder
PhyloNetworks.recursionPreOrder
PhyloNetworks.recursionPreOrder!
PhyloNetworks.removeHybrid!
PhyloNetworks.resetEdgeNumbers!
PhyloNetworks.resetNodeNumbers!
PhyloNetworks.rezip_canonical!
PhyloNetworks.sameTaxa
PhyloNetworks.sampleBootstrapTrees
PhyloNetworks.sampleCFfromCI
PhyloNetworks.setBLGammaParsimony!
PhyloNetworks.setBranchLength!
PhyloNetworks.setGammaBLfromGammaz!
PhyloNetworks.setGammas!
PhyloNetworks.setNonIdBL!
PhyloNetworks.setalpha!
PhyloNetworks.seteigeninfo!
PhyloNetworks.seteigeninfo!
PhyloNetworks.seteigeninfo!
PhyloNetworks.seteigeninfo!
PhyloNetworks.seteigeninfo!
PhyloNetworks.setlengths!
PhyloNetworks.setparameters!
PhyloNetworks.setpinv!
PhyloNetworks.setpinvalpha!
PhyloNetworks.setrates!
PhyloNetworks.showQ
PhyloNetworks.showdata
PhyloNetworks.shrink2cycleat!
PhyloNetworks.shrink3cycleat!
PhyloNetworks.shrinkedge!
PhyloNetworks.sort_stringasinteger!
PhyloNetworks.startingBL!
PhyloNetworks.startingrate
PhyloNetworks.startree_newick
PhyloNetworks.symmetricnet_newick
PhyloNetworks.symmetricnet_newick
PhyloNetworks.symmetrictree_newick
PhyloNetworks.synchronizePartnersData!
PhyloNetworks.taxadiff
PhyloNetworks.traitlabels2indices
PhyloNetworks.traverseContainRoot!
PhyloNetworks.undoGammaz!
PhyloNetworks.unzip_canonical!
PhyloNetworks.unzipat_canonical!
PhyloNetworks.updateBL!
PhyloNetworks.updateContainRoot!
PhyloNetworks.updatePostOrder!
PhyloNetworks.updatePreOrder!
PhyloNetworks.updateSSM!
PhyloNetworks.updateSSM_root!
PhyloNetworks.update_logtrans
PhyloNetworks.update_logtrans
PhyloNetworks.updatecache_edge!
PhyloNetworks.updateconstraintfields!
PhyloNetworks.updateconstraints!
PhyloNetworks.writeTopologyLevel1
StatsAPI.coeftable
StatsAPI.confint
StatsAPI.deviance
StatsAPI.deviance
StatsAPI.fit
StatsAPI.loglikelihood
StatsAPI.nobs
StatsAPI.nulldeviance
StatsAPI.stderror
StatsAPI.vcov
StatsModels.isnested
Types
PhyloNetworks.BinaryTraitSubstitutionModel
PhyloNetworks.DataCF
PhyloNetworks.EqualRatesSubstitutionModel
PhyloNetworks.HKY85
PhyloNetworks.HybridNetwork
PhyloNetworks.JC69
PhyloNetworks.ParamsBM
PhyloNetworks.ParamsMultiBM
PhyloNetworks.PhyloNetworkLinearModel
PhyloNetworks.Quartet
PhyloNetworks.RateVariationAcrossSites
PhyloNetworks.RateVariationAcrossSites
PhyloNetworks.ReconstructedStates
PhyloNetworks.ShiftNet
PhyloNetworks.TraitSimulation
PhyloNetworks.TraitSubstitutionModel
PhyloNetworks.TwoBinaryTraitSubstitutionModel
PhyloNetworks.ANode
PhyloNetworks.BM
PhyloNetworks.CacheGammaLiNC
PhyloNetworks.CacheLengthLiNC
PhyloNetworks.CacheLengthLiNC
PhyloNetworks.ContinuousTraitEM
PhyloNetworks.EdgeT
PhyloNetworks.MatrixTopologicalOrder
PhyloNetworks.Node
PhyloNetworks.NucleicAcidSubstitutionModel
PhyloNetworks.OptSummary
PhyloNetworks.PagelLambda
PhyloNetworks.QuartetNetwork
PhyloNetworks.QuartetT
PhyloNetworks.ScalingHybrid
PhyloNetworks.StatisticalSubstitutionModel
PhyloNetworks.StatisticalSubstitutionModel
PhyloNetworks.SubstitutionModel
PhyloNetworks.TopologyConstraint
PhyloNetworks.TopologyConstraint
PhyloNetworks.WithinSpeciesCTM