Files in phangorn

Phylogenetic Reconstruction and Analysis

README.md R/RcppExports.R R/plotBS.R R/mast.R R/hash_phylo.R R/distSeq.R R/hadamard.R R/phyDat_conversion.R R/read.nexus.splits.R R/consensusNet.R R/read.nexus.partitions.R R/discrete.gamma.R R/dist.p.R R/pml_control.R R/pmlPen.R R/codon.R R/transferBootstrap.R R/codonTest.R R/treeManipulation.R R/maxCladeCred.R R/networx.R R/clanistic.R R/delta.score.R R/pml_bb.R R/plot_pml.R R/F3X4.R R/addConfidences.R R/pmlMix.R R/plot_networx.R R/linkfun.R R/lento.R R/pml_generics.R R/modelTest.R R/plotAnc.R R/gap_as_state.R R/splits.R R/SOWH.R R/phangorn-package.R R/phyDat.R R/ltg2amb.R R/read.phyDat.R R/Densi.R R/treedist.R R/splitsNetwork.R R/phylo.R R/ancestral.R R/upgma.R R/image_phyDat.R R/treeRearrangement.R R/bootstrap.R R/distTree.R R/SH.R R/neighborNet.R R/zzz.R R/draw_CI.R R/candidate_tree.R R/bipart.R R/Coalescent.R R/superTree.R R/parsimony.R R/phyDat2.R R/baseFreq.R R/pmlPart.R R/fitch64.R R/sankoff.R R/cladePar.R R/joint_ASR.R R/bab.R R/simSeq.R inst/doc/Trees.Rmd inst/doc/IntertwiningTreesAndNetworks.R inst/doc/Ancestral.Rmd inst/doc/MLbyHand.Rmd inst/doc/Networx.R inst/doc/Trees.R inst/doc/AdvancedFeatures.Rmd inst/doc/AdvancedFeatures.R inst/doc/Morphological.R inst/doc/Ancestral.R inst/doc/Morphological.Rmd inst/doc/Networx.Rmd inst/doc/MLbyHand.R inst/doc/IntertwiningTreesAndNetworks.Rmd inst/tinytest/test_hash.R inst/tinytest/test_SH.R inst/tinytest/test_superTree.R inst/tinytest/test_mast.R inst/tinytest/test_phyDat.R inst/tinytest/test_pmlCluster.R inst/tinytest/test_hadamard.R inst/tinytest/test_Clanistics.R inst/tinytest/test_pmlPart.R inst/tinytest/test_distances.R inst/tinytest/test_codon.R inst/tinytest/test_parsimony.R inst/tinytest/test_pmlMix.R inst/tinytest/test_pml.R inst/tinytest/test_readnexus_multi.R inst/tinytest/test_speciesTree.R inst/tinytest/test_candidate_tree.R inst/tinytest/test_pml_generics.R inst/tinytest/test_treeManipulation.R inst/tinytest/test_bootstrap.R inst/tinytest/test_add_edge_length.R inst/tinytest/test_dist_tree.R inst/tinytest/test_treedist.R inst/tinytest/test_ancestral.R inst/tinytest/test_pmlPen.R inst/tinytest/test_splits.R inst/tinytest/test_treeRearrangement.R inst/tinytest/test_modelTest.R tests/testthat.R tests/tinytest.R tests/testthat/test_plot_networx.R tests/testthat/test_plot_pml.R tests/testthat/test_plot_ancestral.R vignettes/Trees.Rmd vignettes/Ancestral.Rmd vignettes/MLbyHand.Rmd vignettes/AdvancedFeatures.Rmd vignettes/Morphological.Rmd vignettes/Networx.Rmd vignettes/IntertwiningTreesAndNetworks.Rmd man/dist.hamming.Rd man/codonTest.Rd man/midpoint.Rd man/nni.Rd man/dfactorial.Rd man/mast.Rd man/dist.p.Rd man/chloroplast.Rd man/superTree.Rd man/delta.score.Rd man/phangorn-internal.Rd man/neighborNet.Rd man/Laurasiatherian.Rd man/reexports.Rd man/as.splits.Rd man/write.ancestral.Rd man/as.phyDat.Rd man/yeast.Rd man/transferBootstrap.Rd man/cladePar.Rd man/pml.Rd man/baseFreq.Rd man/simSeq.Rd man/plot.pml.Rd man/treedist.Rd man/writeDist.Rd man/phangorn-package.Rd man/image.phyDat.Rd man/distanceHadamard.Rd man/SH.test.Rd man/add_edge_length.Rd man/ancestral.pml.Rd man/modelTest.Rd man/identify.networx.Rd man/upgma.Rd man/pmlCluster.Rd man/phyDat.Rd man/parsimony.Rd man/hadamard.Rd man/gap_as_state.Rd man/read.phyDat.Rd man/coalSpeciesTree.Rd man/densiTree.Rd man/add_ci.Rd man/NJ.Rd man/pmlMix.Rd man/consensusNet.Rd man/bootstrap.pml.Rd man/pml_bb.Rd man/designTree.Rd man/SOWH.test.Rd man/getClans.Rd man/add.tips.Rd man/addConfidences.Rd man/mites.Rd man/plot.ancestral.Rd man/read.nexus.splits.Rd man/write.pml.Rd man/discrete.gamma.Rd man/pml.control.Rd man/dna2codon.Rd man/CI.Rd man/latag2n.phyDat.Rd man/pml.fit.Rd man/allTrees.Rd man/splitsNetwork.Rd man/bab.Rd man/maxCladeCred.Rd man/Ancestors.Rd man/lento.Rd man/plot.networx.Rd man/cophenetic.networx.Rd man/as.networx.Rd man/plotBS.Rd man/read.nexus.partitions.Rd man/pmlPart.Rd