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      ellenS
      Participant

      Hello everyone!
      I have a set of bacterial 16SrRNA sequences (about 50 non-coding sequences) that Id like to align in order to reconstruct a phylogenetic tree. I use MUSCLE to make a multiple sequence alignment. My Question is how to treat with the gaps in the MSA? Am I supposed to trim the ends of the sequences?
      Thank you in advance
      Ellen

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