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Using PyNAST as standalone program / PyNAST alternatives?

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  • Using PyNAST as standalone program / PyNAST alternatives?

    Hej

    I am working on an Illumina paired-end Amplicon workflow. Now I need to align my unique reads in order to produce a phylogeny what in QIIME would be done with the align_seqs.py command, followed by the filter_alignment.py.

    However, I'd like to avoid to use Qiime just for this step because the workflow is R based (DADA2) and Qiime can't be called from R (afaik)

    I know there are R packages around (e.g. msa) but as I understand they don't take reference alignments and are considerably slower.

    I tried installing PyNAST but the website says that it requires a specific UCLUST version that in turn doesn't seem to run on the newest OSX.

    So my questions are:

    - is there a way to run PyNAST as stand-alone and not from within QIIME
    - are there good an fast alternatives (preferably ones that also provide a tutorial on sensible default settings)
    - Is it preferable to use a reference alignment when generating a multiple sequence alignment for short (~420 bp) reads?

    thanks for the help!
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