AdvancedQueryOptionContainer

Seed search algorithm (0=double-indexed/1=query-indexed/ctg=contiguous-seed)

Use chaining with extension.

Band for dynamic programming computation

Flag: --bootstrap

Use chaining without extension

Scaling factor for the chaining gap penalty.

Scaling factor for the chaining skip penalty.

Flag: --check-multi-target

Minimum range overlap with higher scoring hit to delete a hit (default=50%)

Flag: --cut-bar

Extension algorithm (wfa, ksw=default)

Flag: --family-map

File: --family-map-query

Mask seeds based on frequency

Number of standard deviations for ignoring frequent seeds.

E-value threshold for gapped filter (auto)

Flag: --heartbeat

Minimum number of identities for stage 1 hit.

Only consider seed hits against longest target for identical seeds.

Only consider seed hits against longest query for identical seeds.

Flag: --log-evalue-scale

Ignore translated sequences without an open reading frame of at least this length.

Initialize multiprocessing run.

Process only a single query chunk as specified

Enable continuation of interrupted multiprocessing run.

Flag: --mp-self

enable distributed-memory parallel processing

BlastN mismatch penalty

Flag: --query-or-subject-cover

Flag: --query-parallel-limit

Percentage of query range to be covered for range culling.

Filter out top FLOAT fraction of repetitive minimizers.

BlastN match reward

Flag: --roc-file

Add the query length to the SAM format (tag ZQ).

Cutoff for seed complexity.

Seed shapes

Set the match score of stop codons against each other.

Enable target-indexed mode.

Maximum number of targets to report per species.

Flag: --unaligned-targets

xDrop for ungapped alignment.

Use gnl|BL_ORD_ID| style format in XML output.

zDrop for gapped dna alignment