Biopython offers much better support for the PhyloXML format. It also builds more aesthetic and seemingly accurate phylograms through its distance calculation and tree building, presumably by leveraging a different distance algorithm. I compared several trees built using R packages (phangorn, ape, seqinr) and Biopython, all rooted trees created with the UPGMA algorithm from a distance matrix, and the ones generated by Biopython are preferred. I did not compare identical algorithms, however, as the ones available in Biopython are preferred anyway and some weren't in R's packages.
Biopython offers much better support for the PhyloXML format. It also builds more aesthetic and seemingly accurate phylograms through its distance calculation and tree building, presumably by leveraging a different distance algorithm. I compared several trees built using R packages (
phangorn,ape,seqinr) and Biopython, all rooted trees created with the UPGMA algorithm from a distance matrix, and the ones generated by Biopython are preferred. I did not compare identical algorithms, however, as the ones available in Biopython are preferred anyway and some weren't in R's packages.