veryfasttree is ignoring nuclotide sequences

[ian-yunus]

I am aligning nucleotide sequences, but veryfasttree doesn't recognize it. it ignores all a t g c n characters... What to do?

veryfasttree -nt test.aln > test.nwk
Command: veryfasttree -nt test.aln
VeryFastTree Version 4.0.3 (OpenMP, SSE4.1) with SSE3
Alignment: test.aln
Nucleotide distances: Jukes-Cantor 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: Jukes-Cantor, CAT approximation with 20 rate categories
OMP: Info #276: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
Ignored unknown character a (seen 4192215 times)
Ignored unknown character c (seen 4952186 times)
Ignored unknown character g (seen 4965808 times)
Ignored unknown character n (seen 5765 times)
Ignored unknown character t (seen 4185136 times)
WARNING! ONLY 0.0% NUCLEOTIDE CHARACTERS -- IS THIS REALLY A NUCLEOTIDE ALIGNMENT?

[cesarpomar]

Not all input formats are case-insensitive, so please check that your input meets the case requirements.

[Rohit-Satyam]

@ian-yunus It's super easy to change the cases of Nucleotide in you alignment from small to capitals using seqkit as follows using -u parameter and usually takes seconds:

seqkit seq -u realign.aln > output.aln