I have a table with the frequencies and counts of all the identified OTUs (up to species level) within my samples and I would like to construct a phylogenetic tree in R. I am familiar with the packages I need. Still, I do not know the table format in which I should organise my data to create a phylogenetic tree. Maybe the ITS next to each OTU?
Thank you in advance!
Xabier Vázquez-Campos
You need at least representative sequences for each OTU.However, if you are working with ITS sequences better forget about it. Unless you are working with a single genus, the ITS is useless for phylogeny due to lack of conservancy. Fine as a barcoding sequence, but not really suited for phylogenetics in general.
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