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fhcrc / taxtastic

Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
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look into incorporating greengenes taxonomy into taxtastic #35

Closed nhoffman closed 1 year ago

nhoffman commented 13 years ago

see

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002566

also,

Todd Desantis says that one can download all sequences here: http://greengenes.lbl.gov/Download/Sequence_Data/Greengenes_format/greengenes16SrRNAgenes.txt.gz and infer taxonomy from lineages.

If it seems feasible, allow user to choose between NCBI and greengenes taxonomies in taxit.

cmccoy commented 13 years ago

@nhoffman: the 45-greengenes-taxonomy branch is making a database using the file @matsen pointed me to: http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/Caporaso_Reference_OTUs/gg_otus_4feb2011.tgz

There's no NCBI taxonomy information, at present.

nhoffman commented 1 year ago

No plans to do this at this point