Hot answers tagged rrna
4
OK, first of all do not use CLustalX to align the sequences. It is a very old algorithm and is outperformed by just about any modern aligner (including its descendent, clustal omega, and t-coffee, mafft, kalign etc etc).
As for 1) that depends on what you want to do, there is no perfect solution. What question are you trying to answer? If you want a tree ...
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