I am creating a phylogenetic tree to compare how diverse is a species that I have collected from different parts of my country. I have decided to take 4 phylogenetic markers (CYTB, COX1, 16S and 12S) and work with them. But at the moment of creating the tree, it is strange to see all the markers of each sample. How should I process the data to make the phylogenetic tree?
This is a bit unclear. How did you get your first tree? What is your specific problem?
What do you mean when you say it is "strange to see the markers of each sample"?
Didn't you concatenate the sequences before the analysis?
Species A: CYTB, COX1, 16S, 12S
Species B: CYTB, COX1, 16S, 12S
Species C: CYTB, COX1, 16S, 12S
Just as Jens Rohwer said, first, align each marker separately then you will need to concatenate the sequences to form a single "super-alignment" file. this will serve as the new input sequence for your phylogenetic tree.
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