Making tree with only the best placement?

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Michael Doane

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Mar 21, 2018, 11:19:01 PM3/21/18
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Thank you for all the help thus far on the PhyloSift journey.

When placing the sequences onto the tree, those placements which produce some probability are reported, with some sequencing producing several placements. For purposes of making phylogenetic diversity measures of this tree, is there a way to make only a tree in which the placement with the highest probability is kept? I thought maybe Guppy could do this, but I am not seeing a command which reads only the top placement for each read, then makes the diversity measure. Is there a way to manipulate the .jplace after it has been produced by PhyloSift? Or is there a command that I am not interpreting properly when running 'all' mode of phylosift?

Again, thank you for all the help thus far.

Mike

Guillaume Jospin

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Mar 21, 2018, 11:41:08 PM3/21/18
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Hi Mike,
I'm not sure how one would do that manipulating the jplace file.
This might be a question for the pplacer/guppy guys.

Phylosift does not provide an option to only report the top probability. Only threshold of that sort comes in earlier in the pipeline but there is still a good chance that placement will have multiple possibilities.

Sorry I can't be of more help.

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