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fstrozzi / scalability-reproducibility-chapter

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explore alternatives to pal2nal #2

Open mr-c opened 7 years ago

mr-c commented 7 years ago

https://scicrunch.org/scicrunch/data/source/nlx_143912-1/search?q=pal2nal

pjotrp commented 7 years ago

I wrote a command line version of pal2nal with https://github.com/pjotrp/bioruby-alignment and tested that with clustal-omega. E.g. install bio-alignment

gem install bio-alignment

run pal2nal with

pal2nal aa.aln nt.fa --no-validate

(you may need to find the gem_path binaries). Without validation you get the exact same result that pal2nal.pl for PAML. Good thing PAML has a proper license these days.