PanTools version 3.4.0
======================

PanTools is a toolkit for comparative analysis of large number of
genomes. It is developed in the Bioinformatics Group of Wageningen
University, the Netherlands. Please cite the relevant publication(s)
from the list of publications if you use PanTools in your research.

Licence
-------

PanTools has been licensed under `GNU GENERAL PUBLIC LICENSE version 3.
<https://www.gnu.org/licenses/gpl-3.0.en.html>`_

Publications
------------

-  `PanTools: representation, storage and exploration of pan-genomic
   data.
   <https://academic.oup.com/bioinformatics/article/32/17/i487/2450785>`_
-  `Efficient inference of homologs in large eukaryotic pan-proteomes
   <https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2362-4>`_
-  `Pan-genomic read mapping
   <https://www.biorxiv.org/content/10.1101/813634v1>`_
-  `The Pectobacterium pangenome, with a focus on Pectobacterium
   brasiliense, shows a robust core and extensive exchange of genes
   from a shared gene pool
   <https://doi.org/10.1186/s12864-021-07583-5>`_
-  `Pantools v3: functional annotation, classification, and phylogenomics
   <https://doi.org/10.1093/bioinformatics/btac506>`_

Functionalities
---------------

PanTools currently provides these functionalities:

-  Construction of a panproteome
-  Adding new genomes to the pangenome
-  Adding structural/functional annotations to the genomes
-  Detecting homology groups based on similarity of proteins
-  Optimization of homology grouping using BUSCO
-  Read mapping
-  Gene classification
-  Phylogenetic methods

Requirements
------------

-  \ **Java Virtual Machine**\  version 1.8 or higher, Add path to the
   java executable to your OS path environment variable.
-  \ **KMC**\ : A disk-based k-mer counter, After downloading the
   appropriate version (linux, macos or windows), add path to the *kmc*
   and *kmc_tools* executables to your OS path environment variable.
-  \ **MCL**\ : The Markov Clustering Algorithm, After downloading and
   compiling the software, add path to the *mcl* executable to your OS
   path environment variable.

For installing and configuring all required software, please see our
:doc:`install` page.

Running the program
-------------------

Add the path to the java archive of PanTools, located in the
*pantools/target* subdirectory, to the OS path environment variable.
Then run PanTools from the command line by:

.. code:: bash

   $ java <JVM options> -jar pantools-3.4.0.jar <subcommand> <arguments>

| **Useful JVM options**
| - **-server** : To optimize JIT compilations for higher performance
| - **-Xmn(a number followed by m/g)** : Minimum heap size in mega/giga
  bytes
| - **-Xmx(a number followed by m/g)** : Maximum heap size in mega/giga
  bytes

Contents
--------

.. toctree::
   :maxdepth: 1

   install
   construct
   characterize
   phylogeny
   msa
   explore
   mapping
   query
   differences
   Tutorial 1 - Install PanTools <tutorial_part1>
   Tutorial 2 - Construct pangenome <tutorial_part2>
   Tutorial 3 - Neo4j browser <tutorial_part3>
   Tutorial 4 - Characterization <tutorial_part4>
   Tutorial 5 - Phylogeny <tutorial_part5>
   
PanTools has its documentation hosted on Read the Docs.