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This repository has been archived by the owner on Nov 9, 2023. It is now read-only.
@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differences) that show that the trees generated using either the Greengenes 85% aligned reference OTU sequences or the (outdated) Greengenes aligned core set as the reference database are effectively identical.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.
The text was updated successfully, but these errors were encountered:
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...
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).
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.
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).
@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.
The text was updated successfully, but these errors were encountered: