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?
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?
Hi,
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 ran:
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?
Thank you!