use Greengenes 85% aligned reference OTUs instead of (outdated) Greengenes core set as default PyNAST template

[gregcaporaso]

@wasade did some comparisons about a year ago, and I did some comparisons today (see here, which I'll be updating shortly to contain more test sequences, but I don't expect differences) that show that the trees generated using either the Greengenes 85% aligned reference OTU sequences or the (outdated) Greengenes aligned core set as the reference database are effectively identical.

So, we're going to update to use the Greengenes 13_8 85% OTU aligned sequences as the default template alignment for PyNAST, as it's more recently updated, we have a clearer understanding of how they were created, and the licensing is clearer.

If anyone has concerns about this, please reply here.

[wasade]

👍

[gregcaporaso]

In my updated results looking at ~3000 representative sequences from the Moving Pictures dataset, the correlation coefficient is a bit lower, but still highly significant. We do lose fewer sequences as failing to aligned with GG, so on that measure those results are better...

Thoughts on this?

[wasade]

If you blast a handful of those seqs, do they hit anything that makes sense
in nt?

On Wed, Dec 10, 2014 at 12:42 PM, Greg Caporaso notifications@github.com
wrote:

In my updated results looking at ~3000 representative sequences from the Moving
Pictures dataset, the correlation coefficient is a bit lower, but still
highly significant. We do lose fewer sequences as failing to aligned with
GG, so on that measure those results are better...

Thoughts on this?

—
Reply to this email directly or view it on GitHub
#1770 (comment).

[gregcaporaso]

I think you're misunderstanding - sequences that were failing to hit with the (ancient) core set are now hitting the GG 85% reference OTUs, so on the metric of minimizing sequences that fail to align with PyNAST, the GG 85% OTUs are doing better as a template alignment.

I'm asking whether anyone is concerned about the Mantel correlation between the tip-to-tip distance matrices from the resulting trees is only ~0.72.

[wasade]

Oh, okay, that's awesome

On Wed, Dec 10, 2014 at 1:15 PM, Greg Caporaso notifications@github.com
wrote:

I think you're misunderstanding - sequences that were failing to hit with
the (ancient) core set are now hitting the GG 85% reference OTUs, so on the
metric of minimizing sequences that fail to align with PyNAST, the GG 85%
OTUs are doing better.

I'm asking whether anyone is concerned about the Mantel correlation
between the tip-to-tip distance matrices from the resulting trees is only
~0.72.

—
Reply to this email directly or view it on GitHub
#1770 (comment).

[jairideout]

Fixed in #1777.