PanTools version |ProjectVersion| ================================= 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. `_ Publications ------------ - `Pantools v3: functional annotation, classification, and phylogenomics `_ - `The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool `_ - `Pan-genomic read mapping `_ - `Efficient inference of homologs in large eukaryotic pan-proteomes `_ - `PanTools: representation, storage and exploration of pan-genomic data. `_ 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:`/getting_started/install` page. Running the program ------------------- Make sure you can run java on your command line. Then you can run PanTools from the command line by: .. substitution-code-block:: bash $ java -jar pantools-|ProjectVersion|.jar | **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 Options ------- All options except for ``--version`` also apply to all subcommands. .. list-table:: :widths: 30 70 * - ``--version``/``-V`` - Display version info. * - ``--help``/``-h`` - Display a help message for pantools or any subcommand. * - ``--manual``/``-M`` - Open the manual for pantools or any subcommand in a local browser. * - ``--force``/``-f`` - Force. For instance, force overwrite a database with ``build_pangenome``. * - ``--no-input`` - Ignore prompts or any other interactive user input. * - ``--debug``/``-d`` - Show debug messages in the console. * - ``--quiet``/``-q`` - Only show warnings or higher level logging messages in the console. Contents -------- .. toctree:: :caption: Getting Started :maxdepth: 1 Install getting_started/differences getting_started/workflows getting_started/selection getting_started/query .. toctree:: :caption: Pangenome Construction :maxdepth: 1 construction/build construction/annotate construction/group construction/synteny .. toctree:: :caption: Pangenome Analysis :maxdepth: 1 analysis/blast analysis/classification analysis/explore analysis/gene_retention analysis/go_enrichment analysis/metrics analysis/msa analysis/phylogeny analysis/mapping analysis/sequence_visualization analysis/support analysis/dn_ds .. toctree:: :caption: Tutorial :maxdepth: 1 Tutorial 1 - Install PanTools Tutorial 2 - Construct pangenome Tutorial 3 - Neo4j browser Tutorial 4 - Characterization Tutorial 5 - Phylogeny .. toctree:: :caption: Developer guide :maxdepth: 1 Installation Release steps Database structure