The effect of alignment uncertainty substitution models and priors in building and dating the mammal tree of life

摘要

A flow chart of data preparation and analyses conducted in this study. The original mammal alignments were trimmed and filtered, generating 4 sets of alignments - before trimming (BT), after trimming (AT), filtered by the protocol of Irisarri et al. (FP), and further filtered by comparing ML trees with the concatenation tree (FM). In the data analyses, different alignments and substitution models were used to evaluate the effects of alignment uncertainty and the choice of substitution models on phylogenomic inference