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epruesse / SINA

SINA - Reference based multiple sequence alignment
https://sina.readthedocs.io
GNU General Public License v3.0
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Printing Full Phylogeny #75

Closed mbcouger closed 3 years ago

mbcouger commented 4 years ago

Hello Sina Dev Group,

I am using SINA to classify 16s seqs, I am running the following commmand with the newest Silva release: ./sina -i Ecolittest.fasta --db SILVA_132_SSURef_NR99_13_12_17_opt.arb -p 1 --meta-fmt CSV -o tesyh --search-db SILVA_132_SSURef_NR99_13_12_17_opt.arb --lca-fields tax_slv

Can you please point me on how to print the full phyologeny of the alingments (Domain> Species)

Many Thanks, Brian

epruesse commented 4 years ago

Try using --search-max-result 1 - that will work like a best-BLAST and just give you the full classification for that hit.

IBG-5-KIT commented 4 years ago

but what if one does not want a "best-BLAST" but the actual Least common ancestor (LCA) results. Is there a nice way to get the results in table format, similar to the classification output of the Silva ACT webservice?

(because the best-hit is often not entirely reliable)

epruesse commented 4 years ago

Yes, there is now. Try the newest version with -o results.csv and -f set to the fields you want to have.

epruesse commented 3 years ago

SINA 1.7.0 binaries should be up within the hour, and the Bioconda packages within the day. Give those a shot and reopen this if necessary.