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Introduction
Technical Requirements
Third Party Software
Contents
Terminology
Database
Fisher Algorithm
Single Gene Trees
Getting Started
Installation
Download Provided Dataset
Prepare Custom Dataset
Quickstart
Metadata Explanation
Detailed Example Workflow
Project Directory Setup
Homolog Collection
Gene Tree Construction
Tree Parsing
Apply to Database
Taxa and Gene Selection
Matrix Construction
Utilities
aa_comp_calculator.py
aa_recoder.py
astral_runner.py
backup_restoration.py
bipartition_examiner.py
build_database.py
explore_database.py
fast_site_remover.py
fast_taxa_remover.py
genetic_code_examiner.py
heterotachy.py
mammal_modeler.py
nucl_matrix_constructor.py
purge.py
random_resampler.py
rtc_binner.py
taxon_collapser.py
Frequently Asked Questions
References
Table of contents
Project Directory Setup
Homolog Collection
Gene Tree Construction
Tree Parsing
Apply to Database
Taxa and Gene Selection
Matrix Construction