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name: alignment-search-and-phylogeny description: "Operate Biopython alignment, search result, BLAST, and phylogeny workflows with offline-safe routing guidance." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

Alignment, search, BLAST, and phylogeny router

Use this sub-skill when the task is primarily about Biopython alignment/search/tree APIs:

• score or recover pairwise sequence alignments with Bio.Align.PairwiseAligner;
• load or apply substitution matrices such as BLOSUM62;
• inspect Bio.Align.Alignment objects or route multiple-alignment file handling through Bio.AlignIO;
• parse, index, filter, or write sequence-search output with Bio.SearchIO;
• parse or write BLAST XML with Bio.Blast, or plan a carefully approved Bio.Blast.qblast call;
• read, traverse, query, reroot, prune, ladderize, or write phylogenetic trees with Bio.Phylo.

Do not use this sub-skill for general sequence/FASTQ/GenBank conversion, Entrez or other database retrieval, or structural superposition. Route those tasks to the package skill areas for file I/O, web/database workflows, or structural bioinformatics.

First-pass routing

1. Pairwise alignment or substitution scoring: load references/alignment-search-workflows.md and choose PairwiseAligner; use legacy Bio.pairwise2 only for migrating old code.
2. Multiple alignment file input/output: use Bio.AlignIO guidance in references/alignment-search-workflows.md; route broad conversion/indexing questions to the file-I/O sub-skill.
3. Search program results: load references/searchio-blast-reference.md; prefer SearchIO for BLAST tabular/XML, BLAT PSL, HMMER, FASTA m10, Infernal, Exonerate, HH-suite, and InterProScan result models.
4. BLAST XML records or qblast: load references/searchio-blast-reference.md; keep parsing offline unless the user explicitly authorizes network use and supplies required service etiquette metadata.
5. Trees and phylogenies: load references/phylo-reference.md; copy trees before destructive modifications if the original topology must be preserved.
6. Failures, unexpected scores, parser errors, or optional tools: load references/troubleshooting.md.

Offline check

Run scripts/alignment_phylo_smoke.py in an environment with Biopython installed to verify core offline coverage for PairwiseAligner, substitution matrices, SearchIO model availability, and Phylo Newick parsing/traversal/modification. The script does not require network access, external executables, databases, or original repository files.