R语言(phangorn)与进化树Phylogenetics-in-R-with-phangorn

PhylogeneticsinRpackagephangornKlausSchliepUMPC,MNHNMarch18,2010PhylogeneticsinRpackagephangornKlausSchliepOutlineIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryPhylogeneticsinRpackagephangornKlausSchliepOutlineIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryPhylogeneticpackagesinRThistalkismainlyaboutthetwopackagesapeandphangorn.TherearemanyotherphylogeneticpackagesonCRAN(someareforveryspecictasks)e.g.:Iphylobase(niceplotfunctions),apTreeshape,geiger,ouch,ade4anoverviewovermanypackagesisgivenat::IseqinrIShortRead(bioconductor)Imanybioconductorpackagesformeta-data,annotationsetc.PhylogeneticsinRpackagephangornKlausSchliepOutlineIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryOverviewofR-packagesforphylogeneticsphylogenyreconstruction:Iape(NJ,fastme)Iphangorn(ML,MP,Networkmethods,Hadamard)IHierarchicalclusteringhclustinpackagestatsupgmaisjustawrapperaroundhclustPhylogeneticsinRpackagephangornKlausSchliepOutlineIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryphangornPhylogeneticsinRpackagephangornKlausSchliepOutlineIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryLoadingdataread.dnainapereadsinnucleotidedata(phylipandfasta),read.aaaminoacidsandread.nexus.datanexusles.ThelesareeitherofclassDNAbinoralistdata-read.dna(data.phy)data-read.dna(data.fas,format=fasta)data-read.nexus.data(data.nex)data-as.phyDat(data)data-read.phyDat(data,format=phylip,+type=DNA)read.phyDatisawrapperaroundtheotherfunctionandtransformsobjectintoclassphyDat.Nexuslescomeinlotofdierentdialects.Splitstreehasaquitegoodnexusparser,soimportingintoandexportingfromSplitstreeoftenhelpstomakethemreadabletoothersoftware.PhylogeneticsinRpackagephangornKlausSchliepOutlineIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryLoadingtreesapealsooerstofunctionstoreadintrees:Iread.treeforreadingtreesinNewickformatIread.nexusforreadingtreesinNexusformatTherearealsosomefunctionstoconvertbetweendierenttreeformatsinR,e.g.hclust.PhylogeneticsinRpackagephangornKlausSchliepOutlineIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryDistancemethodsTherearemanydierentdistancebasedmethodsavailablenj,fastme.balandfastme.olsinapeandupgma,wpgmainphangorn(basedoncodefromhclust)library(phangorn)library(multicore)data(Laurasiatherian)dm=dist.dna(as.DNAbin(Laurasiatherian),+model=JC69)treeUPGMA=upgma(dm)treeNJ=nj(dm)treeFME=fastme.bal(dm)PhylogeneticsinRpackagephangornKlausSchliepOutlineIntroductionPhylogeneticswithphangorn(andape)ImportingdataandtreesDistancemethodsMaximumParsimonyMaximumLikelihoodOnetreecan'trulethemallComparingtreePartitionModelsHadamardConjugationandSplitsSimulatingtreesandsequencesSummaryPlottingtreesWecanplotthesetreespar(mfrow=c(2,2),mar=c(2,2,4,+2))plot(treeUPGMA)title(UPGMA)plot(treeUPGMA,type=fan)title(UPGMA(fan))plot(treeNJ,type=unrooted,main=NJ)title(NJ)plot(treeFME,type=unrooted,main=fastME)title(fastME)PlatypusWallarooPossumBandicootOpposumArmadilloElephantAardvarkTenrecHedghogGymnureMoleShrewRbatFlyingFoxRyFlyFoxFruitBatLongTBatHorseDonkeyWhiteRhinoIndianRhinPigAlpacaCowSheepHippoFinWhaleBlueWhaleSpermWhaleRabbitPikaSquirrelDormouseGuineaPigMouseVoleCaneRatBaboonHumanLorisCebusCatDogHarbSealFurSealGraySealUPGMAPlatypusWallarooPossumBandicootOpposumArmadilloElephantAardvarkTenrecHedghogGymnureMoleShrewRbatFlyingFoxRyFlyFoxFruitBatLongTBatHorseDonkeyWhiteRhinoIndianRhinPigAlpacaCowSheepHippoFinWhaleBlueWhaleSpermWhaleRabbitPikaSquirrelDormouseGuineaPigMouseVoleCaneRatBaboonHumanLorisCe