Collection of commonly used RDP Tools for easy building
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AbundanceStats @ c690a6f Added biom cluster output formats when get clustering stats May 27, 2014
AlignmentTools @ 9230ba6 Fixed a bug in pairwise alignment tool, now check reverse orientation… Oct 30, 2015
Clustering @ a0490b0 Modified FrameBot de novo algorithm May 27, 2015
Framebot @ 32cac09 Minor updates in FrameBot and KmerFilter to set Locale to English to … Dec 22, 2015
KmerFilter @ 002c053 Minor updates in FrameBot and KmerFilter to set Locale to English to … Dec 22, 2015
PrimerDesign @ 8e340b5 Update Primer Design Aug 2, 2018
ProbeMatch @ 1948013 Added new command options to ProbeMatch package Jun 5, 2014
ReadSeq @ b967aa7 update ReadSeq package Jul 21, 2016
SeqFilters @ 76814eb Updated SeqFilter with bug fixes Feb 18, 2015
SequenceMatch @ d9e902f Many updates in multiple packages. Main updates including Xander asse… Feb 11, 2015
TaxonomyTree @ 8a971c3 Added many new features to classifier package Jun 6, 2014
Xander-HMMgs @ 5237c8f Added mercy-kmer approach to keep the critical singleton kmers when k… Apr 24, 2015
Xander_assembler @ 36d84c1 Minor updates in FrameBot and KmerFilter to set Locale to English to … Dec 22, 2015
classifier @ 701e229 Fixed a typo in Classifier source code Sep 15, 2015
.gitignore Updated README and makefile Jun 17, 2013
.gitmodules added primer design Mar 29, 2017
Makefile Many updates in multiple packages. Main updates including Xander asse… Feb 11, 2015
README ant version requirement Apr 3, 2017

README

Metaproject for RDP Tools

This project includes the modules from the RDP (Classifier, Clustering, SequenceMatch, ProbeMatch, InitialProcessing, FrameBot, ReadSeq, Xander) and all their dependencies. Don't click "Download ZIP" button, instead, copy the cloneURL and type 
git clone cloneURL

After cloning this repository enter the commands

## Initial Project Set Up
$ git submodule init
$ git submodule update

then type 'make'

Jars are placed in the main directory, you can run them with

java -jar classifier.jar|Clustering.jar|...

Building depends on 'make' and 'ant 1.9'. 

## Update Existing Project
$ git pull
$ git submodule update
$ make clean
$ make

## Usage

The RDP Paired-end Reads Assembler used in the publication (Cole et al., 2014 Nucl. Acids Res.) is available at http://rdp.cme.msu.edu/misc/resources.jsp

See each individual tool page or fungene_pipeline (https://github.com/rdpstaff/fungene_pipeline) to run one or multiple tools.