TABLE 1.
An overview of the software and methods presented throughout the review, divided by the methodological incongruence they attempt to address.
| Name | Software or method? | Citation |
|---|---|---|
| Model selection | ||
| Modeltest‐NG | Software | Darriba et al. (2020) |
| ModelFinder | Software | Kalyaanamoorthy et al. (2017) |
| Akaike information criterion | Method | Parzen et al. (1988) |
| Bayesian information criterion | Method | Neath and Cavanaugh (2011) |
| Rogue sequence | ||
| RoguenaRok | Software | Aberer et al. (2011) |
| Phyutility | Software | Smith and Dunn (2008) |
| Booster | Software | Lemoine et al. (2018) |
| Bootstrapping | Method | Hillis and Bull (1993) |
| Partition addition bootstrap approach | Method | Struck et al. (2006) |
| Permutation test | Method | Thornton and Desalle (2000) |
| Leaf stability index | Method | Thorley and Wilkinson (1999) |
| Transfer bootstrap | Method | Lemoine et al. (2018) |
| Problematic sequences | ||
| Canary sequence method | Method | Fleming et al. (2020) |
| Partition Coalescence support | Method | Chandonia et al. (2004) and Liu et al. (2010) |
| Contamination | ||
| Blobtools | Software | Laetsch and Blaxter (2017) |
| CroCo | Software | Simion et al. (2018) |
| Paralogy | ||
| OrthoMCL | Software | Li et al. (2003) |
| PhylotreePruner | Software | Kocot et al. (2013) |
| TreSpeX | Software | Struck (2014) |
| Branch length heterogeneity | ||
| K‐score | Software | Soria‐Carrasco et al. (2007) |
| Treeshrink | Software | Mai and Mirarab (2018) |
| Aligroove | Software | Kück et al. (2014) |
| Slow‐fast method | Method | Brinkmann and Philippe (2008) |
| Long branch score | Method | Struck (2014) |
| Locus‐specific sequence subsampling | Method | Rivera‐Rivera and Montoya‐Burgos (2016, 2019) |
| Compositional heterogeneity and site saturation | ||
| Phylobayes posterior predictive tests | Software | Lartillot et al. (2009) |
| BaCoCa | Software | Kück and Struck (2014) |
| SRH test | Method | Naser‐Khdour et al. (2019) |
| Chi‐squared test for compositional heterogeneity | Method | Cummings (2004) |
| RCFV | Method | Kück and Struck (2014) |
| Patristic distance linear regression | Method | Nosenko et al. (2013) |
| Convergence values | Method | Kück and Struck (2014) |
| Saturation index | Method | Duchêne et al. (2021) |
| Recoding strategies | Method | Hernandez and Ryan (2019) and Smith et al. (2009) |