uppercase option about phyling

[chtsai0105]

This was being addressed by the phylotree module, all sequences are forced uppercase before sending to VeryFastTree.

PHYling/src/phyling/phylotree.py

Lines 43 to 45 in 4da4a3a

	for line in f.read().splitlines():
	if not line.startswith(">"):
	line = line.upper()

But we can definitely do that earlier in output msa results. I was just not sure if the lowercase is meaningful so I simply preserve it.