Hi,
For diversity analyses, which methods should i use for constructing a phylogenetic tree? The sepp method or align-to-tree-mafft-fasttree ? What are the differences ?
Good morning Ana,
I think sepp is the recommended method right now. It's newer, and arguably think better.
MAFFT is more classic, so some researchers may prefer that.
Colin
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I really like SEPP, it feels like the best of both words: working out an established backbone and getting new clustering.
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But do you know the difference between those methods? I tried with both and the Pcoas were kind of different.
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In MAFTT, you make a new tree by aligning the sequences against themselves. In SEPP, the sequences get aligned and inserted into an existing black bone. The SEPP paper might be good to review, since it shows some examples and talks about why.
Best,
Justine
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