Use when running iterative sequence-to-sequence HMMER searches to expand a protein family from one or a few seed sequences against a sequence database.
jackhmmer/home/vimalinx/miniforge3/envs/bio/bin/jackhmmerreferences/help.mdphmmer search can usually recover.hmmsearch when you already have a profile HMM, and hmmscan when the target is an HMM database.# 1) Iterative search with parseable hit tables
jackhmmer \
--tblout hits.tbl \
--domtblout domains.tbl \
-N 5 \
--cpu 8 \
query.fa \
targets.fa
# 2) Save the accepted-hit alignment from the search rounds
jackhmmer \
-N 3 \
-A accepted_hits.sto \
query.fa \
targets.fa
# 3) Tighten inclusion thresholds during iterative expansion
jackhmmer \
-N 5 \
--incE 1e-5 \
--incdomE 1e-5 \
query.fa \
targets.fa
--tblout and --domtblout outputs on the first run so iteration effects are inspectable.-N and set explicit inclusion thresholds if family drift would be costly.hmmbuild or downstream annotation.libopenblas.so.0 is missing, so fix the runtime environment before expecting live execution.jackhmmer takes positional arguments in query-then-database order; the target <seqdb> cannot be a non-rewindable stdin stream.jackhmmer does not accept curated --cut_ga, --cut_nc, or --cut_tc threshold modes.