About CRAIC

Author

CRAIC is written and maintained by James McInerney, Department of Evolution, Ecology and Behaviour, University of Liverpool (ORCID 0000-0003-1885-2503).

More of his software and research is at https://mol-evol.github.io/.

How to cite CRAIC

If you use CRAIC in your research, please cite:

McInerney J. 2026. CRAIC: interactive interrogation of multiple sequence alignment uncertainty. bioRxiv preprint (link to follow).

The paper is under review. This page will give the journal citation once it is published; until then, please cite the preprint.

@article{mcinerney2026craic,
  author  = {McInerney, James},
  title   = {{CRAIC}: interactive interrogation of multiple sequence alignment uncertainty},
  journal = {bioRxiv},
  year    = {2026},
  note    = {Preprint; link to follow}
}

The same citation is in the app (Help ▸ About CRAIC and how to cite it…, which can copy it for you) and behind GitHub's Cite this repository button on the repository; craic --version and craic --help point to this page.

Please cite the methods you use, too

CRAIC puts other people's methods in front of you. If your results depend on one of them, cite it as well:

the pair-HMM posteriors and consistency transformation: ProbCons (Do et al., 2005, Genome Research 15:330–340);
any external aligner you ran through CRAIC: MAFFT, MUSCLE, Clustal Omega, ClustalW, ProbCons or PRANK;
rule-based trimming: trimAl (Capella-Gutiérrez et al., 2009) or Gblocks (Castresana, 2000); outlier sequences: OD-seq (Jehl et al., 2015).

Licence

Bugs and suggestions

Please open an issue at https://github.com/mol-evol/craic/issues.