Constructing and analyzing phylogenetic trees is central to biological disciplines such as evolutionary and systematic biology. Accurate phylogenetic inference improves the estimation of evolutionary relationships, rates of molecular evolution, and Operational Taxonomic Units (OTUs). Careful alignment of sequence data is critical prior to any phylogenetic reconstruction, and there are many different multiple sequence alignment programs that are currently used (reviewed in Edgar & Batzoglou 2006). However, difficulty persists when using alignments to accurately determine actual genetic divergences. A major, yet under-explored, problem is saturation: the repetition of base substitutions at a single site within a sequence. Saturation causes issues because numerous substitutions in sequences within an alignment can erroneously underestimate divergence. Here, we present an algorithm, Splinter, that identifies and accounts for saturation during DNA sequence alignment.
Weedop, K. Bodie and Pearse, William D., "Multiple Sequence Alignment While Assessing Saturation Across Sequence Data" (2017). Biology Posters. Paper 165.