Multiple sequence alignment

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ellenS
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Multiple sequence alignment

Post by ellenS » Wed May 17, 2017 11:06 am

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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