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Updated: Aug 5, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Improved gene tree inference from removing alignment errors both from focal genes and when training substitution
Andrew L Wheeler1, Chiragdeep Chatur2, Peter W Goodman3
1Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, Arizona 85721, USA.
Molecular Biology and Evolution
|July 27, 2026
Summary
A new method, CLOAK (CLeaning On the basis of Alignment C(K)onsensus), gently removes errors from Multiple Sequence Alignments (MSAs). This improves phylogenetic tree inference, especially for single gene MSAs.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Biology
Background:
- Multiple Sequence Alignment (MSA) is crucial for phylogenetic analysis but susceptible to errors.
- Existing alignment cleaning algorithms may remove informative residues, negatively impacting phylogenetic tree inference.
Purpose of the Study:
- Introduce CLOAK (CLeaning On the basis of Alignment C(K)onsensus), a novel algorithm for cleaning MSAs.
- Evaluate CLOAK's performance as a gentle MSA filter compared to existing methods.
Main Methods:
- CLOAK utilizes consensus across MSAs generated by various Hidden Markov Models and guide trees.
- Performance was assessed using BALiBASE benchmarks and by evaluating improvements in gene tree inference for single copy orthologs.
Main Results:
- CLOAK demonstrates a low false positive rate, effectively removing alignment errors while preserving informative residues.
- Gentle filtering, as implemented by CLOAK, showed superior performance in improving gene tree inference for single gene MSAs compared to stringent filtering.
Conclusions:
- CLOAK offers an effective and gentle approach to MSA cleaning, balancing error removal with the preservation of crucial data.
- The choice of MSA filtering stringency is critical and task-dependent, with gentle filtering being advantageous for single gene MSA analysis and phylogenetic tree inference.
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