blastdb-aliastool

name	blastdb-aliastool
description	Use when creating BLAST database aliases, converting GI files to binary format, or aggregating multiple BLAST databases into a single virtual database.
disable-model-invocation	true
user-invocable	true

blastdb-aliastool

Quick Start

• Command: blastdb_aliastool -db dbname -gilist ids.txt -out alias_name
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blastdb_aliastool
• Version: 2.17.0+
• Full reference: See references/help.md

When To Use This Tool

• Create a virtual alias that points to a restricted subset of an existing BLAST database.
• Aggregate multiple BLAST databases of the same molecule type into one logical database.
• Convert legacy GI or SeqID lists into binary list formats for faster reuse.
• Build taxon-, accession-, or curated-subset views without rebuilding the source BLAST DB.

Common Patterns

# 1) Restrict a protein database by sequence IDs
blastdb_aliastool \
  -db nr \
  -dbtype prot \
  -seqidlist ids.txt \
  -out nr_subset \
  -title "NR subset"

# 2) Aggregate several protein databases into one alias
blastdb_aliastool \
  -dblist "db1 db2 db3" \
  -dbtype prot \
  -out combined_db \
  -title "Combined BLAST DB"

# 3) Convert a text seqid list into binary form
blastdb_aliastool \
  -seqid_file_in ids.txt \
  -seqid_db nr \
  -seqid_dbtype prot \
  -seqid_file_out ids.bsl

Recommended Workflow

1. Decide whether you are restricting one database, aggregating several databases, or converting a list format.
2. Prepare the needed list files and confirm the source BLAST DB type (nucl or prot).
3. Create the alias or binary list file and then test it immediately with a small BLAST query.
4. Keep the alias definition next to the source databases so it stays resolvable in downstream environments.

Guardrails

• The executable on disk is named blastdb_aliastool, even though this skill is named blastdb-aliastool.
• Aggregated databases must all be the same molecule type; the tool does not validate that for you.
• -gilist, -seqidlist, -taxidlist, and -oid_masks are alternative restriction modes, not options you usually combine.
• -dblist and -dblist_file require -out, -dbtype, and -title.
• GI-based workflows are legacy; prefer SeqID or taxonomy-based restriction for modern pipelines when possible.