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CompEvol / beast2

Bayesian Evolutionary Analysis by Sampling Trees
www.beast2.org
GNU Lesser General Public License v2.1
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BEAUti import fasta #66

Closed rbouckaert closed 10 years ago

rbouckaert commented 10 years ago

Would be good for BEAUti to be able to import fasta alignments. Currently, fasta files first have to be converted to nexus before they can be imported.

Perhaps a few other file types should be importable as well.

http://www.hiv.lanl.gov/content/sequence/HelpDocs/SEQsamples.html

has a long list of formats but I'm not sure which ones are the most popular apart from fasta.

tgvaughan commented 10 years ago

Does jebl have parsers for these formats? On Feb 21, 2014 8:05 AM, "rbouckaert" notifications@github.com wrote:

Would be good for BEAUti to be able to import fasta alignments. Currently, fasta files first have to be converted to nexus before they can be imported.

Perhaps a few other file types should be importable as well.

http://www.hiv.lanl.gov/content/sequence/HelpDocs/SEQsamples.html

has a long list of formats but I'm not sure which ones are the most popular apart from fasta.

Reply to this email directly or view it on GitHubhttps://github.com/CompEvol/beast2/issues/66 .

alexeid commented 10 years ago

I don't think we should be in the business of supporting all sorts of different sequence file formats. That is what programs like Geneious are for. FASTA is probably a reasonable (and simple) addition, but if we start adding formats we should probably rely on very well tested existing code where we can as reading the data incorrectly is a nightmare and we shouldn't re-implement things unnecessarily. Lets focus our efforts on problems that haven't already been solved.

Alexei

Sent from my iPhone

On 21/02/2014, at 8:05 AM, rbouckaert notifications@github.com wrote:

Would be good for BEAUti to be able to import fasta alignments. Currently, fasta files first have to be converted to nexus before they can be imported.

Perhaps a few other file types should be importable as well.

http://www.hiv.lanl.gov/content/sequence/HelpDocs/SEQsamples.html

has a long list of formats but I'm not sure which ones are the most popular apart from fasta.

— Reply to this email directly or view it on GitHub.

rbouckaert commented 10 years ago

Agreed, probably not a good idea to support too many formats. I regularly get fasta files from collaborators, so really would like support for that.

rbouckaert commented 10 years ago

issue is fixed but only works from + button in partition panel. Should also work from File/Import menu.