pylogeny.parsimony module

Toolkit for performance of Parsimonious Criterion (Parsimony) methods of optimization of a phylogenetic topology with a particular set of data.

pylogeny.parsimony.fitch(topology, alignment)

Perform the Fitch algorithm on a given tree topology and associated alignment. Deprecated: Python implementation of the Fitch algorithm; see fitch C++ module for a C++ implementation that is roughly four times faster.

pylogeny.parsimony.fitch_cost(topology, profiles)

Calculate the cost using Fitch algorithm on profile set and alignment. Deprecated: Python implementation of the Fitch algorithm; see fitch C++ module for a C++ implementation that is roughly four times faster.

class pylogeny.parsimony.profile_set(alignment)

Hold a set of site_profile profiles for an entire alignment.

__init__(alignment)

Initialize this profile set by indicating an alignment.

Parameters:alignment (an alignment.alignment object) – an alignment object

get(val)

Acquire the site profile at an index.

Parameters:val (an integer) – an index of the set Returns:a site_profile object

getForTaxa(val, tax)

Acquire the string of sequence alphabet characters for a taxon.

Parameters:

• val (an integer) – an index of the set
• tax (a string) – a taxon name

Returns:

a string of characters

weight(val)

Acquire the weight associated with an index.

Parameters:val (an integer) – an index of the set Returns:a weight (integer)

class pylogeny.parsimony.site_profile(alignment, site)

Consolidate a single column of the alignment into a set of components with associated counts.

__init__(alignment, site)

Initialize this profile.

Parameters:

• alignment (an .alignment.alignment object) – an alignment object
• site (an integer) – a site/column index along the alignment