bio-alignment-trimming
Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
npx skills add BioTender-max/awesome-bio-agent-skills --skill alignment-trimming --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: ClipKIT 2.1+, trimAl 1.4+, BMGE 1.12+, Divvier 1.01+, HMMcleaner (current CPAN release of `Bio::MUST::Apps::HmmCleaner`), BioPython 1.83+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `clipkit --version`, `trimal --version`, `BMGE --help`, `Divvier --help` - 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 Trimming **"Remove unreliable columns from this MSA"** → Filter or split columns based on gap fraction, conservation, entropy, or per-residue quality. - CLI: `clipkit`, `trimal`, `BMGE`, `Divvier`, `HMMcleaner` - Python: post-process via Bio.AlignIO with custom column masks **"Make this alignment publication-grade for phylogenetics"** → Apply ClipKIT's `kpic-smart-gap` mode, or trimAl `-automated1`, then verify via tree-stability comparison before vs after trimming. Tool choice and aggressiveness matter more than trimming vs not-trimming. Pick a mode by dataset character (table below),
- Version Compatibility
- Pick a Trimming Mode by Dataset Character
- Goal-Driven Tool Selection
- ClipKIT Modes
- ClipKIT kpic Failure Modes
- trimAl Modes
- BMGE: Block Mapping and Gathering with Entropy
- Divvier: Column Splitting Instead of Removal
- HMMcleaner: Per-Residue Cleaning
- Gblocks: The Legacy Default
- PhyIN: Phylogenetic Incompatibility Trimming
- Decision Tree by Downstream Goal
- TCS Column Masking for Selection Analysis
- MACSE Frameshift Markers Need Post-Processing
clipkit input.fasta -m kpic-smart-gap -o trimmed.fasta clipkit input.fasta -m gappy -g 0.9 -o trimmed.fasta clipkit input.fasta -m kpic-smart-gap --output-format phylip -o trimmed.phy clipkit input.fasta -m kpic-smart-gap --log -o trimmed.fasta trimal -in input.fasta -out trimmed.fasta -automated1 trimal -in input.fasta -out trimmed.fasta -gappyout trimal -in input.fasta -out trimmed.fasta -strictplus -htmlout report.html trimal -in input.fasta -out trimmed.fasta -gt 0.3 -st 0.5 -cons 60 -colnumbering > columns.txt java -jar BMGE.jar -i input.fasta -t AA -of trimmed.fasta -h 0.5 -g 0.2 java -jar BMGE.jar -i input.fasta -t DNA -of trimmed.fasta -m DNAPAM100:2 -h 0.5
What does the bio-alignment-trimming skill do?
Trim multiple sequence alignments using ClipKIT, trimAl, BMGE, Divvier, or HMMcleaner with mode selection guidance per downstream goal. Use when removing unreliable columns or contaminating residues before phylogenetic inference, HMM building, or selection analysis.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill alignment-trimming --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.