RDP Staff

Repositories

• RDPTools

  Collection of commonly used RDP Tools for easy building

  bioinformatics microbiology microbiome bayesian-classifiers 16s sequence-alignment
  Makefile 38 39 18 0 Updated Dec 30, 2020

• Xander-HMMgs
  Java GPL-3.0 2 0 0 0 Updated Dec 29, 2020

• TaxonomyTree

  TaxonomyTree building and traversal utility classes.
  Java GPL-3.0 0 2 0 0 Updated Dec 29, 2020

• SequenceMatch

  K-mer based sequence matching tool
  Java GPL-3.0 2 0 0 1 Updated Dec 29, 2020

• SeqFilters

  Java filtering framework for sequence data
  Java GPL-3.0 1 0 0 0 Updated Dec 29, 2020

• ReadSeq

  Java based common sequence file format reader and sequence file manipulation. Most RDP projects require this package.
  Java GPL-3.0 4 1 0 0 Updated Dec 29, 2020

• ProbeMatch

  Tools for finding (and removing) DNA/RNA primers in sequence reads.
  Java GPL-3.0 1 0 0 0 Updated Dec 29, 2020

• KmerFilter

  Tools for kmer analysis.
  Java GPL-3.0 1 0 1 0 Updated Dec 29, 2020

• Framebot

  Dynamic programming based frame shift detection and correction tool with nearest neighbor classification.
  Java GPL-3.0 7 5 3 0 Updated Dec 29, 2020

• AlignmentTools

  Tools for pairwise sequence comparison, distance calculation, and hidden markov model sequence scoring (using HMMER3 models). Many RDP Projects require this package.
  Java GPL-3.0 2 0 1 0 Updated Dec 29, 2020

• AbundanceStats

  Java code for various ecological abundance statistics
  Java GPL-3.0 0 1 0 0 Updated Dec 29, 2020

• classifier

  RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
  Java GPL-2.0 27 46 20 1 Updated Dec 29, 2020

• EcoFunPrimer

  primer design pipeline

  environment bioinformatics primer-design nucleotide-sequences primerdesign
  Java GPL-3.0 4 2 5 0 Updated Apr 9, 2020

• Clustering

  RDP memory-constrained hierarchical clustering tools.
  Java GPL-3.0 3 1 0 0 Updated Apr 8, 2020

• Xander_assembler

  A gene-targeted assembler tool
  Shell 4 14 5 1 Updated Oct 27, 2017

• fungene_pipeline

  Scripts and resources for analyzing sequence data for select eco-functional genes
  Python 11 8 2 1 Updated May 25, 2017

• kb_rdptools

  kbase app for rdp classifier
  0 0 0 0 Updated Feb 9, 2017

• FungeneUtils

  FungeneUtils package
  Java 0 0 0 0 Updated Jan 10, 2014

• SOAP-examples

  Code samples from various languages for interacting with RDP soap services
  Perl 0 0 0 0 Updated Oct 24, 2012

• gfclassify

  Gene Family Classifier allows for fast and accurate classification of amplicon (or open reading frame) nucleotide sequences.
  JavaScript GPL-3.0 0 2 0 0 Updated Aug 28, 2012