pyro.cme.msu.edu

RDP Rel. 11 Pipeline Tools

Over menu item for popup description;. On the menu item to begin work. Rarr; Pipeline Initial Process. Use the pipeline to process sequence libraries or assemble paired-end reads. CLASSIFIER → RDP Classifier. Assign bacterial/archaeal 16S or fungal 28S rRNA sequences to our taxonomical hierarchy. ALIGNER → Aligner. Align sequences using the fast, secondary-structure aware Infernal aligner. COMPLETE LINKAGE CLUSTERING → Complete Linkage Clustering. Formats for Common Programs:. SHANNON and CHAO1 INDEX.

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RDP Rel. 11 Pipeline Tools | pyro.cme.msu.edu Reviews

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Over menu item for popup description;. On the menu item to begin work. Rarr; Pipeline Initial Process. Use the pipeline to process sequence libraries or assemble paired-end reads. CLASSIFIER → RDP Classifier. Assign bacterial/archaeal 16S or fungal 28S rRNA sequences to our taxonomical hierarchy. ALIGNER → Aligner. Align sequences using the fast, secondary-structure aware Infernal aligner. COMPLETE LINKAGE CLUSTERING → Complete Linkage Clustering. Formats for Common Programs:. SHANNON and CHAO1 INDEX.

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1 rdp pipeline

2 fungene home

3 rdp home

4 hover

5 click

6 data processing steps

7 pipeline initial process

8 analysis tools

9 miscellaneous utilities

10 alignment merger

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RDP Rel. 11 Pipeline Tools | pyro.cme.msu.edu Reviews

https://pyro.cme.msu.edu

Over menu item for popup description;. On the menu item to begin work. Rarr; Pipeline Initial Process. Use the pipeline to process sequence libraries or assemble paired-end reads. CLASSIFIER → RDP Classifier. Assign bacterial/archaeal 16S or fungal 28S rRNA sequences to our taxonomical hierarchy. ALIGNER → Aligner. Align sequences using the fast, secondary-structure aware Infernal aligner. COMPLETE LINKAGE CLUSTERING → Complete Linkage Clustering. Formats for Common Programs:. SHANNON and CHAO1 INDEX.

INTERNAL PAGES

pyro.cme.msu.edu

1

RDP Pipeline Tools

http://pyro.cme.msu.edu/help.jsp;jsessionid=C8070A89438BEB3C085D1F075AB7C955.perry

NEW easy to follow procedural tutorials. NEW Initial Processor stats and charts files. NEW Clustering stats and charts files. Cluster To R Formatter. NEW Aligner stats and charts files. Shannon and Chao1 Index. The V4 FLX forward primer is "AYTGGGYDTAAAGNG" (E. coli position 563-577) and the reverse primers are "TACNVGGGTATCTAATCC", "TACCRGGGTHTCTAATCC", "TACCAGAGTATCTAATTC", "CTACDSRGGTMTCTAATC" (E. coli position 785-802). Some publications that use the above V4 primers:. The analysis pipeline was initi...

2

myRDP Login

http://pyro.cme.msu.edu/seq_select/form.spr;jsessionid=C8070A89438BEB3C085D1F075AB7C955.perry

Your personalized work space. Note about Privacy and Data:. We intend to keep your data private, but your data may be subject to public disclosure due to security issues, programming error, human error, or other reasons. Please keep an up-to-date offline backup of your data at all times. To browse the pipeline tools as a guest please enter the username rdpdemo@demo.edu and password demo. Id (email, lowercase). But data will be erased regularly. 1992-2013 Michigan State University.

3

myRDP Login

http://pyro.cme.msu.edu/clust_format/form.spr;jsessionid=C8070A89438BEB3C085D1F075AB7C955.perry

Your personalized work space. Note about Privacy and Data:. We intend to keep your data private, but your data may be subject to public disclosure due to security issues, programming error, human error, or other reasons. Please keep an up-to-date offline backup of your data at all times. To browse the pipeline tools as a guest please enter the username rdpdemo@demo.edu and password demo. Id (email, lowercase). But data will be erased regularly. 1992-2013 Michigan State University.

4

myRDP Login

http://pyro.cme.msu.edu/chao1/form.spr;jsessionid=C8070A89438BEB3C085D1F075AB7C955.perry

Your personalized work space. Note about Privacy and Data:. We intend to keep your data private, but your data may be subject to public disclosure due to security issues, programming error, human error, or other reasons. Please keep an up-to-date offline backup of your data at all times. To browse the pipeline tools as a guest please enter the username rdpdemo@demo.edu and password demo. Id (email, lowercase). But data will be erased regularly. 1992-2013 Michigan State University.

5

myRDP Login

http://pyro.cme.msu.edu/rarefaction/form.spr;jsessionid=C8070A89438BEB3C085D1F075AB7C955.perry

Your personalized work space. Note about Privacy and Data:. We intend to keep your data private, but your data may be subject to public disclosure due to security issues, programming error, human error, or other reasons. Please keep an up-to-date offline backup of your data at all times. To browse the pipeline tools as a guest please enter the username rdpdemo@demo.edu and password demo. Id (email, lowercase). But data will be erased regularly. 1992-2013 Michigan State University.

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rdp.cme.msu.edu

Tree Builder - Start

http://rdp.cme.msu.edu/treebuilder/treeing.spr

Tree Builder - Start. Your seq cart contains 0 aligned sequences:. Select sequences for treeing using the Hierarchy Browser. Minimum comparable position is 200. This task will take between 6 seconds and 45 minutes depending on how many sequences were selected and server load (During peroids of extremely high server load, you may not be able to submit requests). 1992-2014 Michigan State University Board of Trustees, East Lansing MI 48824. MSU is an affirmative-action, equal-opportunity employer.

rdp.cme.msu.edu

Sequence Match

http://rdp.cme.msu.edu/seqmatch/seqmatch_intro.jsp

You can select sequences from. And Hierarchy Browser to do seqmatch? Percent identity scores will be reported for aligned sequences (limited to 2000). Please enter your sequences:. Choose a file to upload. Cut and paste sequence(s) (in Fasta, GenBank, or EMBL format):. Note: Javascript must be enabled on your browser to use this RDP tool. Type strain information is provided by bacterial taxonomy. View only near-full-length sequences (. 1200 bases), short partials, or both.

rdp.cme.msu.edu

Classifier

http://rdp.cme.msu.edu/classifier/classifier.jsp

NEW procedural tutorials for CLASSIFIER. Classifier now provides gene copy number adjustment. For 16S gene sequences. The 16S gene copy number data is provided by rrnDB. For detailed analysis. The Warcup V2 release notes. Is released in June 2016. How to cite Classifier? The RDP Classifier publication has been selected by Essential Science Indicators as the most-cited paper in a highlighted research area of microbiology. It's featured in December 2011 Science Watch. Please enter your sequences:. MSU is a...

rdp.cme.msu.edu

RDP Tutorial

http://rdp.cme.msu.edu/help/tutorial.jsp

RDP has released NEW PROCEDURAL TUTORIALS. That take you through the basic steps of a web-based sequence analysis workflow with sample and test files. There are also links individual command-line tool instructions to aid in getting sequences ready for further processing. Please give them a try and offer any comments or suggestions for improvement. Begin tutorials here: http:/ rdp.cme.msu.edu/tutorials/RDPtutorial CONTENTS.html. Using RDPTools Output with R/Bioconductor package Phyloseq.

rdp.cme.msu.edu

RDP Release Notes

http://rdp.cme.msu.edu/misc/rel10info.jsp

Ribosomal Database Project Release 11. Please note the RDP License Agreement and how to cite services from this site. RDP Release 11 Notes. Notes and Clarifications About RDP. Release 11 Update History. RDP Release 11 Notes. RDP Release 11 provides many significant enhancements over RDP release 10:. New Data Collection- Fungal 28S rRNA Sequences. New and Updated Alignment. This aligner has several advantages: it incorporates secondary-structure information into the alignment process; as a model-based ali...

rdp.cme.msu.edu

Library Compare

http://rdp.cme.msu.edu/comparison/comp.jsp

Library Compare - Start. Use our library compare tool to do microbial community comparison based on 16S rRNA sequences. This tool uses the RDP naïve Bayesian classifier to provide rapid classification of library sequences into the new phylogenetically consistent higher-order bacterial taxonomy. It estimates the probability of observing the difference in a given taxon using a statistical test. Help topics: Taxonomic Hierarchy Model. Files must be in Fasta, GenBank, or EMBL format). 16S rRNA training set 10.

nightingale.cme.msu.edu

Sequence Match

http://nightingale.cme.msu.edu/seqmatch/seqmatch_intro.jsp

You can select sequences from. And Hierarchy Browser to do seqmatch? Percent identity scores will be reported for aligned sequences (limited to 2000). Please enter your sequences:. Choose a file to upload. Cut and paste sequence(s) (in Fasta, GenBank, or EMBL format):. Note: Javascript must be enabled on your browser to use this RDP tool. Type strain information is provided by bacterial taxonomy. View only near-full-length sequences (. 1200 bases), short partials, or both.

rdp.cme.msu.edu

Hierarchy Browser

http://rdp.cme.msu.edu/hierarchy/hb_intro.jsp

Hierarchy Browser - Start. Note: Javascript must be enabled on your browser to use most RDP tools. Type strain information is provided by bacterial taxonomy. Type strains link taxonomy with phylogeny. Include type strain sequences in your analysis to provide documented landmarks. View only environmental (uncultured) sequences, only sequences from individual isolates, or both. Source classification is based on sequence annotation and the NCBI taxonomy. View only near-full-length sequences (.

fungene.cme.msu.edu

Functional Gene Pipeline / Repository

http://fungene.cme.msu.edu/FunGenePipeline

Over tool menu item for a popup description;. On the tool menu item to begin working with it. PIPELINE → Pipeline. Run a set of sequences through our standard processing pipeline. Rarr; Pipeline Initial Process. Use the RDP Pipeline to process sequence libraries from raw sequencer output to analysis. DEFINED COMMUNITY ANALYSIS → Defined Community Analysis. Perform error analysis of a defined community. DEREPLICATOR → Dereplicator. USEARCH CHIMERA CHECK → Chimera Check. FRAMEBOT → Framebot. Calculate Shan...

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RDP Rel. 11 Pipeline Tools

Over menu item for popup description;. On the menu item to begin work. Rarr; Pipeline Initial Process. Use the pipeline to process sequence libraries or assemble paired-end reads. CLASSIFIER → RDP Classifier. Assign bacterial/archaeal 16S or fungal 28S rRNA sequences to our taxonomical hierarchy. ALIGNER → Aligner. Align sequences using the fast, secondary-structure aware Infernal aligner. COMPLETE LINKAGE CLUSTERING → Complete Linkage Clustering. Formats for Common Programs:. SHANNON and CHAO1 INDEX.

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