gctree documentation

gctree is a command line utility and Python package for using sequence abundance information in phylogenetic inference.

User Guide

• Installation
• Citing gctree
• Quickstart
• Custom tree visualization

CLI Documentation

• gctree
  • Sub-commands
• Parsimony utilities
  • deduplicate
  • mkconfig
  • phylip_parse
• isotype
  • Positional Arguments
  • Named Arguments

API Documentation

• Classes
  • gctree.CollapsedTree
  • gctree.CollapsedForest
• Modules
  • gctree.mutation_model
  • gctree.utils
  • gctree.isotyping
  • gctree.branching_processes

Developer Documentation

• Open source code repository
• Developer tools
• Todo list

Indices and tables

• Index

• Module Index

• Search Page