Question: Commandline alternatives for generating EMBL flat files from NEXUS alignments
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gravatar for Michael G
4.8 years ago by
Michael G50
Germany
Michael G50 wrote:

One of the default tools to generate EMBL flat files from NEXUS-formatted multiple sequence alignments is the "old workhorse" Sequin. I also understand that the genome browser Artemis has a similar functionality, and Artemis is the recommended method for the conversion nex2embl. Neither tool has commandline abilities, however.

The Bio.SeqIO interface in BioPython includes some excellent parsers to read and write the NEXUS multiple alignment and the EMBL flat file formats, respectively. Hence, it provides the functionality necessary to convert NEXUS-formatted DNA sequence alignments into a multi-sequence EMBL flat file.

A similar functionality, I would assume, is provided by BioPerl (but I am not a Perl programmer, so this is just speculation).

Are there any commandline alternatives besides the Python or Perl interpreters to perform the conversion from NEXUS to the EMBL flat file with the intent of generating a submission-ready flat file? For so common a task I would have expected to find more bioinformatic tools, especially on Github.

ADD COMMENTlink modified 6 months ago • written 4.8 years ago by Michael G50
0
gravatar for Michael G
6 months ago by
Michael G50
Germany
Michael G50 wrote:

I eventually wrote a software for that particular purpose: annonex2embl

ADD COMMENTlink written 6 months ago by Michael G50
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