least common ancestor algorithm that is used in lOTUs pipelin (http://psbweb05.psb.ugent.be/lotus/). If used, please cite 1 Hildebrand F, Moitinho-Silva L, Blasche S, et al. Antibiotics-induced monodominance of a novel gut bacterial order. Gut 2019;:gutjnl-2018-317715. doi:10.1136/gutjnl-2018-317715
The preferred mapping input is a custom, query-grouped m8-style whitespace-delimited file with exactly these columns (tabs are conventional):
qseqid, sseqid, pident, length, mismatch, gapopen, qstart, qend, sstart, send, qlen.
A matching header row is optional. Comment lines beginning with # and blank lines are ignored; malformed rows fail with their line number.
For legacy compatibility, the standard 12-column BLAST layout is also accepted:
qseqid, sseqid, pident, length, mismatch, gapopen, qstart, qend, sstart, send, evalue, bitscore.
Legacy rows do not contain qlen, so query-coverage filtering is skipped for them. A file must consistently use one of the two layouts.
Build with a C++20 compiler and zlib using make. The current implementation is single-threaded.
Run the focused correctness checks with make check.
Use -tdep N to read and report a non-default number of taxonomy levels (default: 7). Recognized d__/k__, p__, c__, o__, f__, g__, s__, and t__ prefixes are assigned to their explicit ranks; unprefixed entries retain sequential behavior.