How to create Phylogenetic Trees from fasta files in Python or R? I have around a hundred Fasta files (and will collect several thousand) with DNA sequences and +50x coverage. What is a recommended method to construct a phylogenetic tree? Solutions in Python or R are sought.
I found Phylo from Biopython only handles already calculated trees.
I would not look for a package for this, but instead build a small pipeline calling external tools with something like the following workflow:


Cluster the ~100 sequences with CD-HIT-EST/PSI-CD-HIT or many other options
Take all the sequences that form one individual cluster and build a multiple sequence alignment (MSA) with MAFFT/ClustalOmega or similar
Take the MSA and build a phylogenetic tree with a Maximum-Likelihood approach like iqtree or similar
Visualize the tree file with Jalview or similar


Of course this is rather general and depending on exactly what you're doing you may want a different workflow and/or different tools. You should also explore the parameter space, do not assume the defaults are necessarily good choices