Index

A

append_block() (commonnexus.nexus.Nexus method) apply_to_state() (in module commonnexus.blocks.characters)

as_payload() (commonnexus.blocks.notes.Text method) Assumptions (class in commonnexus.blocks.assumptions) asterisk_is_text (commonnexus.nexus.Config attribute)

B

binarised() (commonnexus.tools.matrix.CharacterMatrix class method)

C

Changeset (class in commonnexus.blocks.sets) CharacterMatrix (class in commonnexus.tools.matrix) CharacterMatrixRow (class in commonnexus.blocks.characters) Characters (class in commonnexus.blocks.characters) characters (commonnexus.tools.matrix.CharacterMatrix property) Charlabels (class in commonnexus.blocks.characters) Charpartition (class in commonnexus.blocks.sets) Charset (class in commonnexus.blocks.sets) Charstatelabel (class in commonnexus.blocks.characters) Charstatelabels (class in commonnexus.blocks.characters) check() (commonnexus.blocks.characters.Dimensions method) (commonnexus.blocks.distances.Dimensions method) Codons (class in commonnexus.blocks.codons) combine() (in module commonnexus.tools.combine) commonnexus.blocks.characters module

commonnexus.blocks.distances module commonnexus.blocks.notes module commonnexus.blocks.sets module commonnexus.blocks.taxa module commonnexus.blocks.trees module commonnexus.tools.combine module commonnexus.tools.matrix module commonnexus.tools.normalise module Config (class in commonnexus.nexus)

D

Data (class in commonnexus.blocks.characters) Datatype (class in commonnexus.blocks.characters) Dimensions (class in commonnexus.blocks.characters) (class in commonnexus.blocks.distances) (class in commonnexus.blocks.taxa)

DistanceMatrixRow (class in commonnexus.blocks.distances) Distances (class in commonnexus.blocks.distances) distinct_states (commonnexus.tools.matrix.CharacterMatrix property) DropChars (class in commonnexus.tools.matrix) DropSpec (class in commonnexus.tools.matrix) duplicate_charlabel() (in module commonnexus.blocks.characters)

E

Eliminate (class in commonnexus.blocks.characters)

encoding (commonnexus.nexus.Config attribute)

F

Format (class in commonnexus.blocks.characters) (class in commonnexus.blocks.distances) format() (commonnexus.blocks.characters.Charlabels method) (commonnexus.blocks.characters.Charstatelabels method) (commonnexus.blocks.characters.Dimensions method) (commonnexus.blocks.characters.Eliminate method) (commonnexus.blocks.characters.Format method) (commonnexus.blocks.characters.Matrix method) (commonnexus.blocks.characters.Options method) (commonnexus.blocks.characters.Statelabels method) (commonnexus.blocks.distances.Dimensions method) (commonnexus.blocks.distances.Format method) (commonnexus.blocks.distances.Matrix method) (commonnexus.blocks.distances.Taxlabels method) (commonnexus.blocks.notes.Picture method) (commonnexus.blocks.notes.Text method) (commonnexus.blocks.sets.Changeset method) (commonnexus.blocks.sets.Charpartition method) (commonnexus.blocks.sets.Charset method) (commonnexus.blocks.sets.Partition method) (commonnexus.blocks.sets.Stateset method) (commonnexus.blocks.sets.Taxpartition method) (commonnexus.blocks.sets.Taxset method) (commonnexus.blocks.sets.Treepartition method) (commonnexus.blocks.sets.Treeset method) (commonnexus.blocks.taxa.Dimensions method) (commonnexus.blocks.taxa.Taxlabels method) (commonnexus.blocks.trees.Translate method) (commonnexus.blocks.trees.Tree static method)

FormatSubcommand (class in commonnexus.blocks.characters) from_characters() (commonnexus.tools.matrix.CharacterMatrix class method) from_commands() (commonnexus.blocks.Block class method) from_data() (commonnexus.blocks.assumptions.Assumptions class method) (commonnexus.blocks.characters.Characters class method) (commonnexus.blocks.distances.Distances class method) (commonnexus.blocks.notes.Notes class method) (commonnexus.blocks.sets.Sets class method) (commonnexus.blocks.taxa.Taxa class method) (commonnexus.blocks.trees.Trees class method) from_fasta() (commonnexus.tools.matrix.CharacterMatrix class method) from_statematrix() (commonnexus.blocks.characters.MatrixData class method)

G

GapMode (class in commonnexus.blocks.characters) get_charstatelabels() (commonnexus.blocks.characters.Characters method) get_matrix() (commonnexus.blocks.characters.Characters method) (commonnexus.blocks.distances.Distances method)

get_taxlabels() (commonnexus.blocks.characters.Characters method) get_texts() (commonnexus.blocks.notes.Notes method)

H

has_gaps (commonnexus.tools.matrix.CharacterMatrix property) has_missing (commonnexus.tools.matrix.CharacterMatrix property)

has_polymorphic (commonnexus.tools.matrix.CharacterMatrix property) has_uncertain (commonnexus.tools.matrix.CharacterMatrix property) hyphenminus_is_text (commonnexus.nexus.Config attribute)

I

ignore_unsupported (commonnexus.nexus.Config attribute) INVALID_SYMBOLS (in module commonnexus.blocks.characters) is_binary (commonnexus.tools.matrix.CharacterMatrix property)

is_binary() (commonnexus.blocks.characters.Characters method) Item (class in commonnexus.blocks.characters) iter_columns() (commonnexus.tools.matrix.CharacterMatrix method) iter_rows() (commonnexus.tools.matrix.CharacterMatrix method)

L

lax_symbols (commonnexus.blocks.characters.Format property)

M

Matrix (class in commonnexus.blocks.characters) (class in commonnexus.blocks.distances) matrix_format (commonnexus.blocks.characters.Characters property) (commonnexus.blocks.distances.Distances property) MatrixData (class in commonnexus.blocks.characters) merged_matrix() (in module commonnexus.tools.combine) module commonnexus.blocks.characters commonnexus.blocks.distances commonnexus.blocks.notes commonnexus.blocks.sets commonnexus.blocks.taxa commonnexus.blocks.trees commonnexus.tools.combine commonnexus.tools.matrix commonnexus.tools.normalise

multistatised() (commonnexus.tools.matrix.CharacterMatrix class method)

N

newick (commonnexus.blocks.trees.Tree property) newick_string (commonnexus.blocks.trees.Tree property)

no_default_matchchar (commonnexus.nexus.Config attribute) normalise() (in module commonnexus.tools.normalise) Notes (class in commonnexus.blocks.notes)

O

Options (class in commonnexus.blocks.characters)

P

Partition (class in commonnexus.blocks.sets)

Picture (class in commonnexus.blocks.notes)

R

remove_block() (commonnexus.nexus.Nexus method) replace_block() (commonnexus.nexus.Nexus method) replace_symbol() (commonnexus.blocks.characters.Format method)

required_cols() (commonnexus.blocks.distances.Format method) resolve_symbols() (commonnexus.blocks.characters.Format method) rooted (commonnexus.blocks.trees.Tree property)

S

Sets (class in commonnexus.blocks.sets) Statelabels (class in commonnexus.blocks.characters) Stateset (class in commonnexus.blocks.sets)

Statesformat (class in commonnexus.blocks.characters) strict (commonnexus.nexus.Config attribute) symbols (commonnexus.tools.matrix.CharacterMatrix property)

T

Taxa (class in commonnexus.blocks.taxa) taxa (commonnexus.tools.matrix.CharacterMatrix property) Taxlabels (class in commonnexus.blocks.distances) (class in commonnexus.blocks.taxa) Taxpartition (class in commonnexus.blocks.sets) Taxset (class in commonnexus.blocks.sets) Text (class in commonnexus.blocks.notes) texts (commonnexus.blocks.notes.Notes property) to_fasta() (commonnexus.tools.matrix.CharacterMatrix method)

to_phylip() (commonnexus.tools.matrix.CharacterMatrix method) Translate (class in commonnexus.blocks.trees) translate() (commonnexus.blocks.trees.Trees method) translate_mapping (commonnexus.blocks.trees.Trees property) Tree (class in commonnexus.blocks.trees) Treepartition (class in commonnexus.blocks.sets) Trees (class in commonnexus.blocks.trees) trees (commonnexus.blocks.trees.Trees property) Treeset (class in commonnexus.blocks.sets) Triangle (class in commonnexus.blocks.distances)

U

Unaligned (class in commonnexus.blocks.unaligned)

V

validate() (commonnexus.blocks.characters.Characters method) (commonnexus.blocks.trees.Trees method)

validate_newick (commonnexus.nexus.Config attribute)