NZGOT v0.0.1 2013-2014
        New Zealand Genomic Observatory Toolkit
                         by
            Walter Xie & Alexei J. Drummond

            Department of Computer Science
                 University of Auckland
                walter@cs.auckland.ac.nz
                alexei@cs.auckland.ac.nz

Last updated: walter@cs.auckland.ac.nz - 30th January 2014

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The toolkit is initially designed to analyse various types of data collected from New Zealand Genomic Observatory project, but we are aimed to integrate these tools to create an open-source framework useful and reusable for data analysis and modelling in bioinformatics and ecology.

The minimum version of Java 1.7 is required. The whole software has the dependencies on JEBL (http://jebl.sourceforge.net) and BEAST 2 (https://github.com/CompEvol/beast2.git). The 3rd party libraries are included in the /lib folder.

Core package in this project is to provide a framework for an easy development of other packages. Its main features are:

• BLAST+ xml output parser (core.blast)
• Ecological modelling concepts, such as OTU, community, diversity, etc. (core.community)
• JEBL Sequence extension, such as translation class (core.sequences)
• Parsers for related UC files [http://www.drive5.com/], such as importer/export, uc parser, etc. (core.community.io, core.io, core.uc)
• utils for DNA sequences, Amino Acid sequences, trees, etc. (core.util)

Each of other packages represents an independent project, but it may share the code with others. Core package is always on the top of dependency, it cannot contain any code of other packages. The available packages at the current version are:

1. Useful tools to rename labels for sequences or tree by regular expressions Main package: nzgo.labelregex Owners: Walter Xie

2. Useful tools for meta-barcoding, such as DNA sequences quality check. Main package: nzgo.metabarcoding Owners: Walter Xie

3. Community matrix analysis. Main package: nzgo.cma Owners: Walter Xie, Alexei Drummond

4. Error correction tool for the next-generation sequencing data. Main package: nzgo.ec Owners: Thomas Hummel, Alexei Drummond, Walter Xie

5. Useful tools for BEAST 2 project. Main package: nzgo.beast Owners: Walter Xie