Emmanuel Paradis

Hi, This is a bug in ape: the conversion from "character" to "DNAbin" does not consider that some values could be `NA`. You can fix this bug 'by hand' since...

I think it's fine. If I remember correctly, the purpose of the NAMESPACE is, among other things, to create R environments with "copies" of (in fact, links towards) of the...

I don't think it's a problem... unless the packages are new and not yet on CRAN... in which case you'll have to decide which one to submit first... a kind...

I see your point: the "egg-chicken" problem will appear when installing! Unless you force the install with install.packages(, dependencies = FALSE) for the 1st one to be installed.

Sounds good. So nothing to change on my side. I guess in your point 2) "ape" should be "adegenet"?

Hello, Try the function `haplotype()` (in pegas too) on your 108 sequences. Once you did it, you can check all sequences are distinct with: ```r h 0) ``` If the...

I suggest you try: ```r all(dist.dna(h, "n", pairwise.deletion = TRUE) > 0) ``` And also: ```r image(h) ``` It seems you read the help page `?haplotype` so that you understand...

It seems you have a very difficult data set, so your inferences will be necessarily limited.

Have a look at this function in ape: `DNAbin2indel`. With it, you can then create a binary matrix indicating presence/absence of indels. `pegas::mjn()` can also analyse binary (0/1) data.

Two other functions from ape that could help you with your data: `latag2n()` and `solveAmbiguousBases()` (maybe you already found them in the meantime). You can try `rmst()` (also in pegas):...