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matsen / pplacer

Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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Reference/query alignment question #353

Closed ghost closed 7 years ago

ghost commented 7 years ago

Hello,

I have two separate fasta files for query sequences and reference sequences, but they are not in the same frame and length. Do you have a recommendation as to what software to use to perform a multiple alignment to put them in the same frame and length? I was thinking of using something like muscle (http://www.ebi.ac.uk/Tools/msa/muscle/) but I wanted to check if there is a better one to use with pplacer.

Thanks, Nick

matsen commented 7 years ago

This is covered here: http://matsen.github.io/pplacer/generated_rst/pplacer.html#making-alignments-for-use-with-pplacer

The commands may be a little out of date. Please suggest edits if that's the case.

http://biocore.github.io/pynast/ is also an option, but I have no experience with that.