For what purpose? It doesn't make any sense to me because they are completely absolute in my view

With this type of question, it helps to link to examples of the input file and desired output file.

your VCF file contains 75 samples. So, generating the 75 DNA sequences will generate a file of 75*3Gb=225 Go (!!)

I only want to use the SNP genotypes (a few thousand) not whole genomes.

A tree like in this pdf, that's what I'm trying to do: ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/low_coverage/snps/low_coverage.2010_06.ychr.report.pdf

PhyML only takes PHYLIP format AFAIK.