Making tree with only the best placement?

Skip to first unread message

Michael Doane

Mar 21, 2018, 11:19:01 PM3/21/18
to PhyloSift
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.


Guillaume Jospin

Mar 21, 2018, 11:41:08 PM3/21/18
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.

You received this message because you are subscribed to the Google Groups "PhyloSift" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To post to this group, send email to
Visit this group at
For more options, visit

Reply all
Reply to author
0 new messages