Emmanuel Paradis

> By the way, I would love to try mjn() that considers both base difference and base deletion/insertion at the same time. That would be revolutionary! There is the difficulty...

You can try to read your data with `read.vcf` (in [pegas](https://github.com/emmanuelparadis/pegas)): the output will be an object of class "loci" that you can convert to the class "genind" with the...

Maybe you called `phymltest()` twice? See `?unique.multiPhylo` to try to check this. Cheers, Emmanuel

It seems like a bug in phyml. Using sequence data from [here](https://emmanuelparadis.github.io/APER/APER2/sylvia.txt), the (shell) command: ``` phyml -i sylvia.txt ``` runs fine and creates the file 'sylvia.txt_phyml_tree.txt' with a single...

Just checked my version number of phyml (under Ubuntu 22): 3:3.3.20211231-1

Hello, You can get the numbers of each haplotype with: ```r Nh

Hi Megha, Very good question! AFAIK, `hw.test` cannot analyse X-linked loci because the formula used in this function assumes all individuals are diploid. If there is another package that implements...

Hi Chris, You seem to have identified the problem correctly. You can try to edit the function yourself. First make a copy in your workspace: ```r mydist

Yes, this function computes the (unscaled) Hamming distance. Maybe each haplotype differs by one SNP?

Hello, First, I guess that what you mean by "dot product" is actually the "matrix product". The dot product (i.e., `sum(x * y)` in R) is commutative, so there would...