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