doc string in treeanc
@@ -31,7 +31,6 @@ class TreeAnc(object):
Parameters
----------
-
tree : str, Bio.Phylo.Tree
Phylogenetic tree. String passed is interpreted as a filename with
a tree in a standard format that can be parsed by the Biopython Phylo module.
@@ -51,18 +50,28 @@ class TreeAnc(object):
filled with the gap sign('-'). If set to True, the end-gaps are converted to "unknown"
characters ('N' for nucleotides, 'X' for aminoacids). Otherwise, the alignment is treated as-is
- ignore_gaps: bool
- Ignore gaps in branch length calculations
+ ref : None, optional
+ Reference sequence used in VCF mode
verbose : int
Verbosity level as number from 0 (lowest) to 10 (highest).
+ ignore_gaps : bool
+ Ignore gaps in branch length calculations
+
+ convert_upper : bool, optional
+ Description
+
seq_multiplicity : dict
If individual nodes in the tree correspond to multiple sampled sequences
(i.e. read count in a deep sequencing experiment), these can be
specified as a dictionary. This currently only affects rooting and
can be used to weigh individual tips by abundance or important during root search.
+ reduce_alignment : bool, optional
+ reduce identical alignment columns to one (not useful when
+ inferring site specific GTR models).
+
**kwargs
Keyword arguments to construct the GTR model
@@ -73,10 +82,9 @@ class TreeAnc(object):
used, which might cause unexpected results.
Raises
- ----------
-
- TypeError
- If a tree is not passed in
+ ------
+ AttributeError
+ If no tree is passed in
"""
