Add rule compute phylogenetic tree

[kbseah]

From @BWobbii: Tree needed to calculate Faith's PD indicator

Notes

• Semicolon character in ASV identifiers may break Newick parser
• for COI we should use a codon-aware aligner like tranalign or MACSE

[BWobbii]

I double-checked phyloseq requirements for the tree format - must be Newick or Nexus yes, codon-aware aligner sounds good!

[kbseah]

@BWobbii i ended up choosing scikit-bio for the Faith's PD calculation, it is from a group of developers who also developed QIIME and BIOM

One question: does rooting the tree influence the index? From what I understand it shouldn't but maybe there is something I have overlooked.

[kbseah]

implemented in #13