Bio.Phylo package
Subpackages
- Bio.Phylo.Applications package
- Module contents
PhymlCommandlinePhymlCommandline.__init__()PhymlCommandline.alphaPhymlCommandline.bootstrapPhymlCommandline.datatypePhymlCommandline.frequenciesPhymlCommandline.inputPhymlCommandline.input_treePhymlCommandline.modelPhymlCommandline.multiplePhymlCommandline.n_rand_startsPhymlCommandline.nclassesPhymlCommandline.optimizePhymlCommandline.parsPhymlCommandline.print_site_lnlPhymlCommandline.print_tracePhymlCommandline.prop_invarPhymlCommandline.quietPhymlCommandline.r_seedPhymlCommandline.rand_startPhymlCommandline.run_idPhymlCommandline.searchPhymlCommandline.sequentialPhymlCommandline.ts_tv_ratio
RaxmlCommandlineRaxmlCommandline.__init__()RaxmlCommandline.parsimony_seedRaxmlCommandline.algorithmRaxmlCommandline.binary_constraintRaxmlCommandline.bipartition_filenameRaxmlCommandline.bootstrap_branch_lengthsRaxmlCommandline.bootstrap_seedRaxmlCommandline.checkpointsRaxmlCommandline.cluster_thresholdRaxmlCommandline.cluster_threshold_fastRaxmlCommandline.epsilonRaxmlCommandline.exclude_filenameRaxmlCommandline.grouping_constraintRaxmlCommandline.modelRaxmlCommandline.nameRaxmlCommandline.num_bootstrap_searchesRaxmlCommandline.num_categoriesRaxmlCommandline.num_replicatesRaxmlCommandline.outgroupRaxmlCommandline.parsimonyRaxmlCommandline.partition_branch_lengthsRaxmlCommandline.partition_filenameRaxmlCommandline.protein_modelRaxmlCommandline.random_starting_treeRaxmlCommandline.rapid_bootstrap_seedRaxmlCommandline.rearrangementsRaxmlCommandline.sequencesRaxmlCommandline.starting_treeRaxmlCommandline.threadsRaxmlCommandline.versionRaxmlCommandline.weight_filenameRaxmlCommandline.working_dir
FastTreeCommandlineFastTreeCommandline.__init__()FastTreeCommandline.bionjFastTreeCommandline.bootFastTreeCommandline.catFastTreeCommandline.closeFastTreeCommandline.constraintWeightFastTreeCommandline.constraintsFastTreeCommandline.expertFastTreeCommandline.fastestFastTreeCommandline.gammaFastTreeCommandline.gtrFastTreeCommandline.gtrfreqFastTreeCommandline.gtrratesFastTreeCommandline.helpFastTreeCommandline.inputFastTreeCommandline.intreeFastTreeCommandline.intree1FastTreeCommandline.logFastTreeCommandline.makematrixFastTreeCommandline.matrixFastTreeCommandline.mlaccFastTreeCommandline.mllenFastTreeCommandline.mlnniFastTreeCommandline.nFastTreeCommandline.njFastTreeCommandline.nniFastTreeCommandline.no2ndFastTreeCommandline.nocatFastTreeCommandline.nomatrixFastTreeCommandline.nomeFastTreeCommandline.nomlFastTreeCommandline.noprFastTreeCommandline.nosupportFastTreeCommandline.notopFastTreeCommandline.ntFastTreeCommandline.outFastTreeCommandline.pseudoFastTreeCommandline.quietFastTreeCommandline.quoteFastTreeCommandline.rawdistFastTreeCommandline.refreshFastTreeCommandline.secondFastTreeCommandline.seedFastTreeCommandline.slowFastTreeCommandline.slownniFastTreeCommandline.sprFastTreeCommandline.sprlengthFastTreeCommandline.topFastTreeCommandline.topmFastTreeCommandline.wag
- Module contents
- Bio.Phylo.PAML package
Submodules
- Bio.Phylo.BaseTree module
TreeElementTreeMixinTreeMixin.find_any()TreeMixin.find_elements()TreeMixin.find_clades()TreeMixin.get_path()TreeMixin.get_nonterminals()TreeMixin.get_terminals()TreeMixin.trace()TreeMixin.common_ancestor()TreeMixin.count_terminals()TreeMixin.depths()TreeMixin.distance()TreeMixin.is_bifurcating()TreeMixin.is_monophyletic()TreeMixin.is_parent_of()TreeMixin.is_preterminal()TreeMixin.total_branch_length()TreeMixin.collapse()TreeMixin.collapse_all()TreeMixin.ladderize()TreeMixin.prune()TreeMixin.split()
TreeCladeBranchColor
- Bio.Phylo.CDAO module
- Bio.Phylo.CDAOIO module
- Bio.Phylo.Consensus module
- Bio.Phylo.NeXML module
- Bio.Phylo.NeXMLIO module
- Bio.Phylo.Newick module
- Bio.Phylo.NewickIO module
- Bio.Phylo.NexusIO module
- Bio.Phylo.PhyloXML module
- Bio.Phylo.PhyloXMLIO module
PhyloXMLErrorread()parse()write()ParserParser.__init__()Parser.read()Parser.parse()Parser.other()Parser.accession()Parser.annotation()Parser.binary_characters()Parser.clade_relation()Parser.color()Parser.confidence()Parser.date()Parser.distribution()Parser.domain()Parser.domain_architecture()Parser.events()Parser.id()Parser.mol_seq()Parser.point()Parser.polygon()Parser.property()Parser.reference()Parser.sequence_relation()Parser.uri()
WriterWriter.__init__()Writer.write()Writer.phyloxml()Writer.other()Writer.phylogeny()Writer.clade()Writer.accession()Writer.annotation()Writer.binary_characters()Writer.clade_relation()Writer.color()Writer.confidence()Writer.date()Writer.distribution()Writer.domain()Writer.domain_architecture()Writer.events()Writer.id()Writer.mol_seq()Writer.node_id()Writer.point()Writer.polygon()Writer.property()Writer.reference()Writer.sequence()Writer.sequence_relation()Writer.taxonomy()Writer.uri()Writer.alt()Writer.branch_length()Writer.lat()Writer.long()Writer.maximum()Writer.minimum()Writer.value()Writer.width()Writer.blue()Writer.duplications()Writer.green()Writer.losses()Writer.red()Writer.speciations()Writer.bc()Writer.code()Writer.common_name()Writer.desc()Writer.description()Writer.location()Writer.name()Writer.rank()Writer.scientific_name()Writer.symbol()Writer.synonym()Writer.type()
- Bio.Phylo.TreeConstruction module
Module contents
Package for working with phylogenetic trees.
See Also: http://biopython.org/wiki/Phylo