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Workum, Dirk-Jan van's avatar
Workum, Dirk-Jan van authored
removing identifiers_incorrect_for_fasttree and uniquifying all sequences that are input for MSA

See merge request !39
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PanTools version 3

PanTools is a pangenomic 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 pangenome
  • Construction of a panproteome
  • Adding new genomes to the pangenome
  • Adding structural annotations to the genomes
  • Detecting homology groups based on similarity of proteins
  • Retrieving features/regions/genomes
  • Read mappping
  • Gene classification
  • Functional annotation incorporation
  • Phylogenetic methods
  • Optimal homology grouping using BUSCO

Cloning this git

For cloning this git, please run:

git clone --recursive https://git.wur.nl/bioinformatics/pantools.git

Building a runnable jar

To build a standalone jar that can be run on any machine with a compatible JVM without any dependencies, install Maven and JDK version 8. Then run mvn package in the PanTools root directory:

mvn package

mvn package will generate two jar files in the target/ directory. The standalone jar file is named pantools-<VERSION>.jar, with <VERSION> being the PanTools version you have checked out. To run it, use (we'll take version 3.3.3 as an example):

java -jar target/pantools-3.3.3.jar

Requirements, Installation, Usage

An extensive manual is available at http://www.bioinformatics.nl/pangenomics/manual/

To use the consensus_tree functionality, PanTools depends on ASTER. For compiling this submodule, please run:

cd ASTER
g++ -std=gnu++11 -march=native -Ofast -pthread astral.cpp -o astral
g++ -std=gnu++11 -march=native -Ofast -pthread astral-pro.cpp -o astral-pro

In case the directory pantools/ASTER is empty, please run the following to retrieve its contents:

git submodule update --init --recursive