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Expand Up @@ -527,15 +527,13 @@ Trimming alignment sites by likelihood
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<div class="hline"></div>

Phylogenetic inference can be highly sensitive to fast-evolving, saturated or
erroneous sites in a sequence alignment. Many studies used Gblocks
([Castresana, 2000]) or trimAl ([Capella-Gutiérrez et al., 2009])
to trim alignment sites prior to phylogenetic reconstruction.
Here, we present an alternative approach called **trimmed log-likelihood**, a
robust phylogenetics method, that automatically detects and trims such sites
during tree search directly.

The trimed log-likelihood method works by dynamically excluding a user-defined proportion of sites
Aligned sites that do not share a common ancestry do not provide useful information for phylogenetic inference. Prequal is designed to remove non-homologous sequences prior to alignment ([Whelan et al., 2018]).

Even when sequences as a whole are homologous, there can still be sites that are not homologous for all sequences in the alignment. Removing whole alignment columns (such as with Gblocks
([Castresana, 2000]) or trimAl ([Capella-Gutiérrez et al., 2009])) can risk losing information about closely related species. Three programs that convert predicted misaligned characters to dashes without removing whole columns are Divvier ([Ali et al., 2019]), Taper ([Zhang et al., 2021]), and CLOAK ([Wheeler et al., 2026]). There is a tradeoff between precision and recall in alignmet filtering, with stricter filters removing more errors, but also removing more correctly aligned characters. These three programs performed best out of the tested alignment filtering methods on a precision recall curve, with Divvier being the strictest filter and CLOAK being the gentlest filter ([Wheeler et al., 2026]).

IQ-Tree contains a method for trimming sites directly during tree search called **trimmed log-likelihood**.
The trimmed log-likelihood method works by dynamically excluding a user-defined proportion of sites
with the lowest log-likelihood values during the tree search. As the search
progresses, the likelihood of each site is recalculated at each step using
current tree and model parameters. This ensures that site removal is always
Expand Down Expand Up @@ -595,4 +593,7 @@ See [Command Reference](Command-Reference) for a complete list of all options av
[Strimmer and Rambaut, 2002]: https://doi.org/10.1098/rspb.2001.1862
[Mayrose et al., 2004]: https://doi.org/10.1093/molbev/msh194
[Yang, 1995]: http://www.genetics.org/content/139/2/993.abstract

[Whelan et al., 2018]: https://doi.org/10.1093/bioinformatics/bty448
[Ali et al., 2019]: https://doi.org/10.1093/molbev/msz142
[Zhang et al., 2021]: https://doi.org/10.1111/2041-210X.13696
[Wheeler et al., 2026]: https://doi.org/10.64898/2025.12.01.691663