alfpy provides command-line Python scripts that let you compare unaligned FASTA sequences (DNA/RNA/protein) with more than 40 distance methods. By default, all distance calculations will output a distance matrix in Phylip format, which can be directly used as an input to popular tree-building software such as PHYLIP or EMBOSS fneighbor.
alfpy is also a Python package that provides alignment-free framework to compare biological sequences and infers their phylogenetic relationships. All its functionalities are wrapped in logically separeted Python modules that let you to write your own analysis scripts with just basic Python knowledge.
If you want to use alfpy as a Python package, here are some examples that should give you an idea of how to use particular modules. To see more examples, please have a look at the docstrings of these modules.