Phylogenetic tree from a reference and DNA reads

Question

[kkrizanovic]

Hello,

I am working on a project concerned with a plant genome.

I've created an assembly from PacBio HiFi reads for one sample, but also have Illumina short DNA reads for two different samples of the same species.

I've calculated the distances between the samples by aligning the Illumina reads to the assembled genome, performing variant calling using freebayes tool and then by counting the variants.

Then I used the distances to draw a simple phylogenetic tree for those three samples.

Could someone tell me is this is correct and is there maybe a better way or some tools that do something like this?