Bio.Nexus package
Submodules
- Bio.Nexus.Nexus module
NexusError
CharBuffer
StepMatrix
safename()
quotestrip()
get_start_end()
combine()
Commandline
Block
Nexus
Nexus.__init__()
Nexus.read()
Nexus.write_nexus_data_partitions()
Nexus.write_nexus_data()
Nexus.append_sets()
Nexus.export_fasta()
Nexus.export_phylip()
Nexus.constant()
Nexus.cstatus()
Nexus.weighted_stepmatrix()
Nexus.crop_matrix()
Nexus.bootstrap()
Nexus.add_sequence()
Nexus.insert_gap()
Nexus.invert()
Nexus.gaponly()
Nexus.terminal_gap_to_missing()
- Bio.Nexus.Nodes module
- Bio.Nexus.StandardData module
- Bio.Nexus.Trees module
TreeError
NodeData
Tree
Tree.__init__()
Tree.node()
Tree.split()
Tree.search_taxon()
Tree.prune()
Tree.get_taxa()
Tree.get_terminals()
Tree.is_terminal()
Tree.is_internal()
Tree.is_preterminal()
Tree.count_terminals()
Tree.collapse_genera()
Tree.sum_branchlength()
Tree.set_subtree()
Tree.is_identical()
Tree.is_compatible()
Tree.common_ancestor()
Tree.distance()
Tree.is_monophyletic()
Tree.is_bifurcating()
Tree.branchlength2support()
Tree.convert_absolute_support()
Tree.has_support()
Tree.randomize()
Tree.display()
Tree.to_string()
Tree.__str__()
Tree.unroot()
Tree.root_with_outgroup()
Tree.merge_with_support()
consensus()
Module contents
The Bio.Nexus contains a NEXUS file parser and objects to model this data.