Method Summary |
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__init__(self,
input)
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add_sequence (self,
name,
sequence)
Adds a sequence to the matrix. |
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append_sets (self,
exclude,
delete,
mrbayes)
Appends a sets block to <filename>. |
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bootstrap (self,
matrix,
delete,
exclude)
Return a bootstrapped matrix. |
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constant (self,
matrix,
delete,
exclude)
Return a list with all constant characters. |
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crop_matrix (self,
matrix,
delete,
exclude)
Return a matrix without deleted taxa and excluded characters. |
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cstatus (self,
site,
delete,
narrow)
Summarize character. |
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export_fasta (self,
filename,
width)
Writes matrix into a fasta file: (self, filename=None, width=70). |
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gaponly (self,
include_missing)
Return gap-only sites. |
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get_original_taxon_order (self)
Included for backwards compatibility. |
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insert_gap (self,
pos,
n,
leftgreedy)
Add a gap into the matrix and adjust charsets and partitions. |
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invert (self,
charlist)
Returns all character indices that are not in charlist. |
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read (self,
input)
Read and parse NEXUS imput (filename, file-handle, string. |
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set_original_taxon_order (self,
value)
Included for backwards compatibility. |
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terminal_gap_to_missing (self,
missing,
skip_n)
Replaces all terminal gaps with missing character. |
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weighted_stepmatrix (self,
name,
exclude,
delete)
Calculates a stepmatrix for weighted parsimony. |
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write_nexus_data (self,
filename,
matrix,
exclude,
delete,
blocksize,
interleave,
interleave_by_partition,
comment,
omit_NEXUS,
append_sets,
mrbayes)
Writes a nexus file with data and sets block. |
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write_nexus_data_partitions (self,
matrix,
filename,
blocksize,
interleave,
exclude,
delete,
charpartition,
comment,
mrbayes)
Writes a nexus file for each partition in charpartition. |
Inherited from object |
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__delattr__ (...)
x.__delattr__('name') <==> del x.name |
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__getattribute__ (...)
x.__getattribute__('name') <==> x.name |
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__hash__ (x)
x.__hash__() <==> hash(x) |
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__new__ (T,
S,
...)
T.__new__(S, ...) -> a new object with type S, a subtype of T |
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__reduce__ (...)
helper for pickle |
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__reduce_ex__ (...)
helper for pickle |
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__repr__ (x)
x.__repr__() <==> repr(x) |
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__setattr__ (...)
x.__setattr__('name', value) <==> x.name = value |
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__str__ (x)
x.__str__() <==> str(x) |