Data from: Graph splitting: a graph-based approach for superfamily-scale phylogenetic tree reconstruction

A protein superfamily contains distantly related proteins that have
acquired diverse biological functions through a long evolutionary history.
Phylogenetic analysis of the early evolution of protein superfamilies is a
key challenge because existing phylogenetic methods show poor performance
when protein sequences are too diverged to construct an informative
multiple sequence alignment. Here, we propose the Graph Splitting (GS)
method, which rapidly reconstructs a protein superfamily-scale
phylogenetic tree using a graph-based approach. Evolutionary simulation
showed that the GS method can accurately reconstruct phylogenetic trees
and be robust to major problems in phylogenetic estimation, such as biased
taxon sampling, heterogeneous evolutionary rates, and long-branch
attraction when sequences are substantially diverged. Its application to
an empirical dataset of the triosephosphate isomerase (TIM)-barrel
superfamily suggests rapid evolution of protein-mediated pyrimidine
biosynthesis, likely taking place after the RNA world. Furthermore, the GS
method can also substantially improve performance of widely used multiple
sequence alignment methods by providing accurate guide trees.