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Old 04-11-2011, 07:16 AM   #6
Palecomic
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Join Date: Aug 2010
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I'd also check out Silva http://www.arb-silva.de/ it's from the guys who made Arb. The plus points are that the alignment is better than greengenes (which uses an old alignment from the Silva group) or RDP (which doesn't bother aligning the variable regions of 16S), the negative points are that aligning more than 300 sequences requires paying for their SINA aligner. You can get round this by aligning using Mothur from Pat Schloss http://www.mothur.org/, doing the alignment there and then merging it with the current Silva database.

You mention that you have a contigs file, which suggests that you're looking at metagenomics data, so perhaps you want to try something like MG RAST http://metagenomics.anl.gov/ or PhylOTU http://www.ploscompbiol.org/article/...l.pcbi.1001061 which will get you phylogenetic information from a metagenomic rather than 16S dataset?
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