This directory contains implementations of various algorithms and tools for analyzing evolutionary fitness and phylogenetic relationships in biological sequences. The main components are:
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.These tools are designed to analyze genetic diversity, infer evolutionary fitness, and understand the shape of genealogical trees in populations.
The code in this directory performs several key functions:
Manages collections of phylogenetic trees:
Analyzes individual phylogenetic trees:
Calculates and analyzes Site Frequency Spectra (SFS):
Provides statistical modeling based on data size:
Visualizes phylogenetic trees and results.
The main entry points for using this codebase are:
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.The codebase relies on several external libraries:
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.Additionally, the code uses custom modules for specific tasks like beta-tree simulation and fitness inference.
The main classes (Forest
, Tree
, SFS
, SizeMatchedModel
) use constructor parameters and method arguments for configuration. Key parameters include:
For Forest
and Tree
:
For SFS
:
For SizeMatchedModel
:
Users can adjust these parameters to customize the analysis for their specific needs in evolutionary studies and population genetics research.
This directory contains implementations of various algorithms and tools for analyzing evolutionary fitness and phylogenetic relationships in biological sequences. The main components are:
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.These tools are designed to analyze genetic diversity, infer evolutionary fitness, and understand the shape of genealogical trees in populations.
The code in this directory performs several key functions:
Manages collections of phylogenetic trees:
Analyzes individual phylogenetic trees:
Calculates and analyzes Site Frequency Spectra (SFS):
Provides statistical modeling based on data size:
Visualizes phylogenetic trees and results.
The main entry points for using this codebase are:
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.The codebase relies on several external libraries:
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.Additionally, the code uses custom modules for specific tasks like beta-tree simulation and fitness inference.
The main classes (Forest
, Tree
, SFS
, SizeMatchedModel
) use constructor parameters and method arguments for configuration. Key parameters include:
For Forest
and Tree
:
For SFS
:
For SizeMatchedModel
:
Users can adjust these parameters to customize the analysis for their specific needs in evolutionary studies and population genetics research.