FAQ

Does ClipKIT trim amino acids, nucleotides, or codons?

ClipKIT trims amino acid and nucleotide alignments. For codon-aligned nucleotide MSAs, --codon keeps trimming decisions in whole codons. The optional --remove_stop_codons mode can first mask terminal, internal, or all in-frame stop codons as gaps.

Is there a website application of ClipKIT?

Currently, ClipKIT is only a command line tool.

If tree inference with no trim works well, why even trim?

Tree inference with trimmed multiple sequence alignments is computationally efficient. In other words, shorter alignments require less computational time and memory during tree search. We found that ClipKIT reduced computation time by an average of 20%. As datasets continuously become bigger, an alignment trimming algorithm that can reduce computational time will be of great value.

What characters are considered gaps?

For amino acids ?, *, -, X; for nucleotides, the same characters and N.

How are ambiguous bases or amino acids handled?

By default, recognized IUPAC ambiguity symbols are treated as missing evidence: they are excluded from entropy/composition and KPI/KPIC state counts and are included in the effective unavailable fraction used by gap-based modes. Use --ambiguity_handling fractional to distribute them equally among possible states for entropy/composition calculations, or literal for the legacy ambiguity interpretation. Configured gap characters take precedence, and ClipKIT does not rewrite the input symbols. See Ambiguity handling for the complete mappings and mode-specific details.

I am having trouble install ClipKIT, what should I do?

Please install ClipKIT using a virtual environment as directed in the installation instructions. If you are still running into issues after installing in a virtual environment, please contact the main software developer via email or twitter.