commonnexus
stable
Contents:
NEXUS Files
Blocks
Tools
Command-line interface
commonnexus
Index
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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M
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N
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O
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P
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R
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S
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T
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U
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V
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__getattribute__() (commonnexus.nexus.Nexus method)
__init__() (commonnexus.nexus.Nexus method)
__str__() (commonnexus.nexus.Nexus method)
__weakref__ (commonnexus.nexus.Nexus attribute)
A
append_block() (commonnexus.nexus.Nexus method)
Assumptions (class in commonnexus.blocks.assumptions)
asterisk_is_text (commonnexus.nexus.Config attribute)
B
blocks (commonnexus.nexus.Nexus property)
C
Changeset (class in commonnexus.blocks.sets)
CharacterMatrix (class in commonnexus.tools.matrix)
Characters (class in commonnexus.blocks.characters)
characters (commonnexus.nexus.Nexus property)
(commonnexus.tools.matrix.CharacterMatrix property)
Charlabels (class in commonnexus.blocks.characters)
Charpartition (class in commonnexus.blocks.sets)
Charset (class in commonnexus.blocks.sets)
Charstatelabels (class in commonnexus.blocks.characters)
Codons (class in commonnexus.blocks.codons)
combine() (in module commonnexus.tools.combine)
comments (commonnexus.nexus.Nexus property)
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)
Dimensions (class in commonnexus.blocks.characters)
(class in commonnexus.blocks.distances)
(class in commonnexus.blocks.taxa)
Distances (class in commonnexus.blocks.distances)
distinct_states (commonnexus.tools.matrix.CharacterMatrix property)
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.trees.Tree static method)
from_characters() (commonnexus.tools.matrix.CharacterMatrix class method)
from_commands() (commonnexus.blocks.Block class method)
from_data() (commonnexus.blocks.characters.Characters class method)
(commonnexus.blocks.distances.Distances class method)
(commonnexus.blocks.notes.Notes class method)
(commonnexus.blocks.taxa.Taxa class method)
(commonnexus.blocks.trees.Trees class method)
from_fasta() (commonnexus.tools.matrix.CharacterMatrix class method)
from_file() (commonnexus.nexus.Nexus class method)
G
get_matrix() (commonnexus.blocks.characters.Characters method)
(commonnexus.blocks.distances.Distances method)
get_numbers() (commonnexus.nexus.Nexus method)
H
hyphenminus_is_text (commonnexus.nexus.Config attribute)
I
ignore_unsupported (commonnexus.nexus.Config attribute)
INVALID_SYMBOLS (in module commonnexus.blocks.characters)
is_binary() (commonnexus.blocks.characters.Characters method)
iter_columns() (commonnexus.tools.matrix.CharacterMatrix method)
iter_rows() (commonnexus.tools.matrix.CharacterMatrix method)
M
Matrix (class in commonnexus.blocks.characters)
(class in commonnexus.blocks.distances)
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)
Nexus (class in commonnexus.nexus)
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)
resolve_set_spec() (commonnexus.nexus.Nexus 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)
strict (commonnexus.nexus.Config attribute)
symbols (commonnexus.tools.matrix.CharacterMatrix property)
T
Taxa (class in commonnexus.blocks.taxa)
taxa (commonnexus.nexus.Nexus property)
(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)
to_fasta() (commonnexus.tools.matrix.CharacterMatrix method)
to_file() (commonnexus.nexus.Nexus method)
Translate (class in commonnexus.blocks.trees)
translate() (commonnexus.blocks.trees.Trees method)
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)
U
Unaligned (class in commonnexus.blocks.unaligned)
V
validate_newick (commonnexus.nexus.Config attribute)
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