Firsly an .aln file feed into PhylML is fine, unless you can program in Python.
Precisely what level of tree building you need depends on its end purpose. Here's past example of a similar question here using NCBI Blast.
Building trees (nj and parsimony) is one of the features of NCBI's Blast. Here's how to do it
- Go to Blast here, https://blast.ncbi.nlm.nih.gov/Blast.cgi
- Enter your sequence into the box (it doesn't accept PDB codes alone)
- Enter the protein database - when I first did this calculation I used SwissProt, thinking there would be alot of sequences - I then used "nr"
Under the algorithm parameters enter "50" (default is too many)
- Hit "Blast"
- Once the search is complete at the top of the page are the hyperlinks: "Other reports: Search Summary [Taxonomy reports] [Distance tree of results]"
- Click on "Distance tree of results"
- This will automatically aligning your sequences and produce, in this case a parsimony based tree, but there is also the option of a nj tree (recommended)
- Click "Tool", "Download", "PDF" ...
Notes
- If you want probabilistic trees, PhylML is certainly one of them, Blast remains quite central to building the alignment.
- With regards building partial genome trees, this will depend on what organism you are studing
- With regards Blast HSPs being treated individually, again it depends on what you question is and generally refers to advanced phylogenetics