.. Funannotate2 documentation master file

Welcome to Funannotate2's documentation!
=======================================

Funannotate2 is a comprehensive eukaryotic genome annotation pipeline that provides a complete workflow for annotating fungal, plant, and other eukaryotic genomes. It integrates various tools and databases to produce high-quality gene predictions and functional annotations.

Key Features
-----------

* Genome cleaning and preparation
* Gene prediction using multiple methods (Augustus, GeneMark-ES, SNAP, GlimmerHMM, etc.)
* Automated ab-initio training of gene prediction algorithms
* Evidence-based gene prediction using transcript andd protein alignment evidence
* Functional annotation using various databases (Pfam, dbCAN, MEROPS, SwissProt, etc.)
* BUSCO-based quality assessment
* Output in various formats (GFF3, GenBank, FASTA, etc.)


Note this documentation was written entirely by augment code's Agent, expect some errors.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   installation
   usage
   clean
   train
   predict
   annotate
   install
   species
   modules
   API
   tutorial
   faq
   changelog

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`