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smirarab / pasta

PASTA (Practical Alignment using SATe and Transitivity)
GNU General Public License v3.0
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Why aren't Saté & Pasta listed in the "External Tools" aligners? #52

Closed hhg7 closed 2 months ago

hhg7 commented 4 years ago

I'm confused by the available aligners with the Pasta GUI, why isn't Saté listed as a possible aligner? Also https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424971/ seems to indicate that PASTA is another aligner itself, instead of a tool for running other aligners? I'm confused because I see MAFFT, GINSI, etc., but not Saté and Pasta

smirarab commented 4 years ago

Aligners are the aligners that can be used within PASTA. PASTA cannot be used within PASTA, neither can SATe. The paper makes it clear that you need a base aligner.

On Tue, May 5, 2020 at 10:45 AM David E. Condon notifications@github.com wrote:

I'm confused by the available aligners with the Pasta GUI, why isn't Saté listed as a possible aligner? Also https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424971/ seems to indicate that PASTA is another aligner itself, instead of a tool for running other aligners? I'm confused because I see MAFFT, GINSI, etc., but not Saté and Pasta

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