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citiususc / veryfasttree

Efficient phylogenetic tree inference for massive taxonomic datasets
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veryfasttree is ignoring nuclotide sequences #23

Open ian-yunus opened 2 months ago

ian-yunus commented 2 months ago

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 commented 2 months ago

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

Rohit-Satyam commented 4 days ago

@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