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aaronmussig / PhyloDM

Efficient calculation of phylogenetic distance matrices.
GNU General Public License v3.0
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A binary #13

Open jianshu93 opened 1 year ago

jianshu93 commented 1 year ago

Hello phylodm team,

it would be nice to have a binary to call from other languages like R, where wrapping rust libraries is not so easy.

Thanks,

Jianshu

aaronmussig commented 1 year ago

Hi Jianshu,

I'm happy to give this a go I've not had any experience in developing R libraries so it may take a bit of time. At a glance, it seems possible.

Cheers, Aaron

jianshu93 commented 1 year ago

Hello Aaron,

Thanks for the response. I was asking because the ape package in R (https://search.r-project.org/CRAN/refmans/ape/html/cophenetic.phylo.html) is very slow when calculating phylogenetic distance among taxa like 16S amplicon (there are many of them in one experiment), microbial ecologists and community ecologists use them quite a lot for the pairwise taxa distance. If it takes a lot of time to wrap in R, I think a single binary that can be called from R scripts also works. It was cited so many times: https://academic.oup.com/bioinformatics/article/20/2/289/204981

Thanks,

Jianshu