Currently SEPP comes with a "global" variable set by the conda install, where Greengenes_13.8 refers to multiple files. This is an intended behavior as we can have other trees: Silva coming soon!!
Anyway, the point is that with this option we could filter all sequences against GG and then build a tree with either GG or Silva.
For reference the current parameters for this 2 options are: "Reference phylogeny for SEPP" & " Positive filtering database"
Currently SEPP comes with a "global" variable set by the conda install, where Greengenes_13.8 refers to multiple files. This is an intended behavior as we can have other trees: Silva coming soon!!
Anyway, the point is that with this option we could filter all sequences against GG and then build a tree with either GG or Silva.
For reference the current parameters for this 2 options are: "Reference phylogeny for SEPP" & " Positive filtering database"