is it possible to get a .jplace file from a phyloseq obj?
Entering edit mode
2.5 years ago
boaty ▴ 200

Hello everyone,

Someone is familiar with pplacer pipeline? I got this phyloseq obj in R which has otu table, tax table, meta table and tree. This obj is generated by DADA2.

Now I want to create a .jplace file from a phyloseq so I made a little research.

  1. jplace is made from pplacer software which has 2 inputs : fasta1 and refpkg. Here I can get fasta1 file from my phyloseq OTU sequence.

  2. But for refpkg file, I need a second software : taxtastic which needs 3 inputs: fasta2 : multiply aligned reference sequences in fasta format, a tree built from fasta2 (newick format) and tree_stats.txt.

  3. And to make a tree_stats.txt file, I need a third tool : phyML which needs 1 input : fasta3 in phylip format.

Here my question is from my 3 fasta files: for now, I have a fasta file comes from the OTU sequence and phyloseq obj has already given a phylogeny tree. But for making .jplace file, I need to redo a multiple alignment from OTU sequence which created a different phylogeny tree.... if I want to make .jplace file, I have to reject the original dada2 tree?

Perhaps, is there some tools already exist which convert phyloseq obj to a .jplace file?

thanks in advance.

tree phyloseq pplacer taxtastic phyml • 482 views

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