Forest
class representing a collection of phylogenetic trees.Tree
class representing individual phylogenetic trees.SFS
(Site Frequency Spectrum) class for analyzing genetic diversity.SizeMatchedModel
class for statistical modeling based on data size.Forest
class: For managing collections of phylogenetic trees.Tree
class: For analyzing individual phylogenetic trees.SFS
class: For calculating and analyzing Site Frequency Spectra.SizeMatchedModel
class: For statistical modeling based on data size.forest.py
: Defines the Forest
class for managing collections of trees.tree.py
: Defines the Tree
class for individual tree analysis.sfs.py
: Defines the SFS
class for Site Frequency Spectrum analysis.size_matched_model.py
: Defines the SizeMatchedModel
class for size-based statistical modeling.ete3
: For phylogenetic tree manipulation and visualization.Bio.Phylo
: For interfacing with Biopython’s phylogenetic tree representation.numpy
: For numerical computations and array manipulations.scipy
: For various scientific computing tasks and statistical functions.pandas
: For data manipulation and analysis.matplotlib
: For visualization of results and trees.Forest
, Tree
, SFS
, SizeMatchedModel
) use constructor parameters and method arguments for configuration. Key parameters include:
Forest
and Tree
:
SFS
:
SizeMatchedModel
: