PanTools version 4.3.2
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
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
Running the program
Install PanTools as described in the Installing PanTools page. You can run PanTools from the command line using:
$ pantools <JVM options> <subcommand> <arguments>
Useful JVM options:
-Xms<heap size>[unit] : Initial heap size in MB (‘m’) or GB (‘g’)
-Xmx<heap size>[unit] : Maximum heap size in MB (‘m’) or GB (‘g’)
-XX:StartFlightRecording=filename=<name>.jfr,disk=true : Enable the Flight Recorder (for developers)
Options
All options except for --version
also apply to all subcommands.
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Display version info. |
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Display a help message for pantools or any subcommand. |
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Open the manual for pantools or any subcommand in a local browser. |
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Force. For instance, force overwrite a database with |
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Ignore prompts or any other interactive user input. |
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Show debug messages in the console. |
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Only show warnings or higher level logging messages in the console. |
Contents
Getting Started
Tutorial PanTools
Pangenome Construction
Pangenome Analysis
Developer guide