Pinned Repositories
AlignmentTools
Tools for pairwise sequence comparison, distance calculation, and hidden markov model sequence scoring (using HMMER3 models). Many RDP Projects require this package.
classifier
RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
EcoFunPrimer
primer design pipeline
Framebot
Dynamic programming based frame shift detection and correction tool with nearest neighbor classification.
fungene_pipeline
Scripts and resources for analyzing sequence data for select eco-functional genes
gfclassify
Gene Family Classifier allows for fast and accurate classification of amplicon (or open reading frame) nucleotide sequences.
RDPTools
Collection of commonly used RDP Tools for easy building
SequenceMatch
K-mer based sequence matching tool
TaxonomyTree
TaxonomyTree building and traversal utility classes.
Xander_assembler
A gene-targeted assembler tool
RDP Staff's Repositories
rdpstaff/classifier
RDP extensible sequence classifier for fungal lsu, bacterial and archaeal 16s
rdpstaff/RDPTools
Collection of commonly used RDP Tools for easy building
rdpstaff/fungene_pipeline
Scripts and resources for analyzing sequence data for select eco-functional genes
rdpstaff/Xander_assembler
A gene-targeted assembler tool
rdpstaff/EcoFunPrimer
primer design pipeline
rdpstaff/Framebot
Dynamic programming based frame shift detection and correction tool with nearest neighbor classification.
rdpstaff/TaxonomyTree
TaxonomyTree building and traversal utility classes.
rdpstaff/gfclassify
Gene Family Classifier allows for fast and accurate classification of amplicon (or open reading frame) nucleotide sequences.
rdpstaff/AbundanceStats
Java code for various ecological abundance statistics
rdpstaff/AlignmentTools
Tools for pairwise sequence comparison, distance calculation, and hidden markov model sequence scoring (using HMMER3 models). Many RDP Projects require this package.
rdpstaff/Clustering
RDP memory-constrained hierarchical clustering tools.
rdpstaff/ProbeMatch
Tools for finding (and removing) DNA/RNA primers in sequence reads.
rdpstaff/ReadSeq
Java based common sequence file format reader and sequence file manipulation. Most RDP projects require this package.
rdpstaff/SequenceMatch
K-mer based sequence matching tool
rdpstaff/FungeneUtils
FungeneUtils package
rdpstaff/kb_rdptools
kbase app for rdp classifier
rdpstaff/KmerFilter
Tools for kmer analysis.
rdpstaff/SeqFilters
Java filtering framework for sequence data
rdpstaff/SOAP-examples
Code samples from various languages for interacting with RDP soap services
rdpstaff/Xander-HMMgs