Bio.Nexus package

Submodules

• Bio.Nexus.Nexus module
  • NexusError
  • CharBuffer
    • CharBuffer.__init__()
    • CharBuffer.peek()
    • CharBuffer.peek_nonwhitespace()
    • CharBuffer.__next__()
    • CharBuffer.next_nonwhitespace()
    • CharBuffer.skip_whitespace()
    • CharBuffer.next_until()
    • CharBuffer.peek_word()
    • CharBuffer.next_word()
    • CharBuffer.rest()
  • StepMatrix
    • StepMatrix.__init__()
    • StepMatrix.set()
    • StepMatrix.add()
    • StepMatrix.sum()
    • StepMatrix.transformation()
    • StepMatrix.weighting()
    • StepMatrix.smprint()
  • safename()
  • quotestrip()
  • get_start_end()
  • combine()
  • Commandline
    • Commandline.__init__()
  • Block
    • Block.__init__()
  • Nexus
    • Nexus.__init__()
    • Nexus.get_original_taxon_order()
    • Nexus.set_original_taxon_order()
    • Nexus.original_taxon_order
    • 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
  • ChainException
  • NodeException
  • Chain
    • Chain.__init__()
    • Chain.all_ids()
    • Chain.add()
    • Chain.collapse()
    • Chain.kill()
    • Chain.unlink()
    • Chain.link()
    • Chain.is_parent_of()
    • Chain.trace()
  • Node
    • Node.__init__()
    • Node.set_id()
    • Node.get_id()
    • Node.get_succ()
    • Node.get_prev()
    • Node.add_succ()
    • Node.remove_succ()
    • Node.set_succ()
    • Node.set_prev()
    • Node.get_data()
    • Node.set_data()
• Bio.Nexus.StandardData module
  • NexusError
  • StandardData
    • StandardData.__init__()
    • StandardData.__len__()
    • StandardData.__getitem__()
    • StandardData.__iter__()
    • StandardData.__next__()
    • StandardData.raw()
    • StandardData.__str__()
• Bio.Nexus.Trees module
  • TreeError
  • NodeData
    • NodeData.__init__()
  • 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.