Question: Using FastTree to Constrian by Taxonomy
gravatar for dmj6ab
2.3 years ago by
dmj6ab10 wrote:

I've recently completed a 16S project using a phylogenetic tree with aligned OTUs from QIIME. I got through the analysis without too many issues, but for the purpose of publication, we would like an "unaligned" tree with a topology that represents only the known taxonomy of a given tip (as opposed to a tree generated from the alignment of 16S data). I saw that in the FastTree workflow, there is the option to constrain the topology FastTree generates based on a matrix of the OTU (or tip/taxa) names and a series of ones and zeroes.

My question is how can I generate a constraint matrix based on known taxonomy without resorting to manual assignment?

I'm pretty new to tree construction so any help would be greatly appreciated, thanks!

ADD COMMENTlink written 2.3 years ago by dmj6ab10

You can write to the author of fasttree who usually replies very fast.

ADD REPLYlink written 2.3 years ago by Cacau470
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