uppercase option

[hyphaltip]

while the lowercase sequences in an alignment match are useful output from HMMER it doens't mean much for the phylogenetic analyses. Tools like VeryFastTree ignore lowercase so it would be better if there was an option to force uppercase sequence writing when reporting concatenated or single alignments I think. Or make uppercase force the default (common use) but allow user to turn this off.

Command: VeryFastTree -double-precision concat_alignments.aa.mfa
VeryFastTree Version 4.0.3 (OpenMP, SSE) Double precision with SSE3
Alignment: concat_alignments.aa.mfa
Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000
Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1
TopHits: 1.00*sqrtN close=default refresh=0.80
ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories
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[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.