bio-alignment-io
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
npx skills add BioTender-max/awesome-bio-agent-skills --skill alignment-io --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Alignment File I/O Read, write, and convert multiple sequence alignment files in various formats. ## Required Import **Goal:** Load modules for reading, writing, and manipulating multiple sequence alignments. **Approach:** Import AlignIO for file I/O and supporting classes for programmatic alignment construction. ```python from Bio import AlignIO from Bio.Align import MultipleSeqAlignment from Bio.SeqRecord import SeqRecord from Bio.Seq import Seq ``` ## Format Coverage Map Three Python libraries cover the alignment-format space, with overlapping but non-identical support. Pick by what is actually required. | Format | `Bio.AlignIO` | `Bio.Align` (modern) | `pyhmmer.easel` | Notes | |--------|---------------|----------------------|-----------------|-------| | Aligned FASTA | R/W | R/W | R/W | Mo
- Version Compatibility
- Required Import
- Format Coverage Map
- Reading Alignments
- Single Alignment File
- Multiple Alignments in One File
- Read as List
- Writing Alignments
- Write Single Alignment
- Write Multiple Alignments
- Write to Handle
- Format Conversion
- Direct Conversion (Most Efficient)
- With Alphabet Specification
What does the bio-alignment-io skill do?
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockholm, FASTA, Nexus, and other alignment formats for phylogenetics and conservation analysis. Use when reading, writing, or converting alignment file formats.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill alignment-io --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.