Can I use pplacer with a tree constructed in Fasttree?
0
0
Entering edit mode
4 months ago
pramirez • 0

Hi All!

I am trying to do phylogenetic placement of S3 amino-acid sequences using Pplacer. I created the reference tree based on a reference alignment of S3 sequences and using Fasttree. Is it possible to use a reference tree from Fasttree? Or is it only possible to use pplacer on trees consturcted using PhyML and RAxML?

Here is the command I used:

pplacer --pretend -r combined_reference.fasta -t S3_modified_tree.txt S3_prodigal_proteins.fasta

And here is the error:

Running pplacer v1.1.alpha19-0-g807f6f3 analysis on S3__prodigal_proteins.fasta... Didn't find any reference sequences in given alignment file. Using supplied reference alignment. Warning: using a statistics file directly is now deprecated. We suggest using a reference package. If you already are, then please use the latest version of taxtastic. Uncaught exception: Failure("please specify a tree model with -s or -c") Fatal error: exception Failure("please specify a tree model with -s or -c")

In case I can use a tree generated in Fasttree. How should be the statistics file formated?

Thanks!

phylogenetics pplacer. fasttree • 129 views
ADD COMMENT

Login before adding your answer.

Traffic: 2661 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6