PMSF trees

These trees were built using the posterior mean site frequency (PMSF) method (Wang et al., 2018) implemented in IQ-TREE. It uses the empirical profile mixture model C60 (Quang et al., 2008) to account for amino acid substitution rate heterogeneity across sites. It is more robust to long-branch attraction (LBA) than site homogeneous models.

Branch supports were generated using ultrafast bootstrap (ufboot) (Hoang et al., 2018), with 1000 replicates (downscaled to integers between 0-100).

Also comes in cons (using up to 100 conserved sites per gene), rand (using 100 randomly selected sites per gene) and rpls (using 30 ribosomal proteins) variants.

Go to GitHub directory.