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thibautjombart / apex

Phylogenetic Methods for Multiple Gene Data
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export to seqinr format #25

Closed thibautjombart closed 9 years ago

thibautjombart commented 9 years ago

for both multidna and multphyDat?

KlausVigo commented 9 years ago

@thibautjombart You mean the alignment class in seqinr? That's a good idea. Just had a short look there exists (non-generic) functions (as.alignment) in both ape and seqinr, which could cause potentially problems if we decide to call ape:::as.alignment. I will write a function in phangorn to do this for phyDat objects, has the advantage that it also should work for amino acids.

thibautjombart commented 9 years ago

Cool!

thibautjombart commented 9 years ago

BTW to stay coherent we probably want to call the functions multidna2alignment and multiphyDat2alignment

KlausVigo commented 9 years ago

Added the functions, at the moment just with concatenate. Requires newest phangorn from github.

thibautjombart commented 9 years ago

Awesome

thibautjombart commented 9 years ago

@KlausVigo I think this will break Travis as it installs CRAN version of the dependencies. Can we \ \dontrun the example?