Extend PartitionFinder to automatically partition DNA and protein alignments.
by Paul Frandsen for National Evolutionary Synthesis Center (NESCent)
ParitionFinder is a piece of phylogenetics software that combines similar sets of sites in a DNA or amino acid alignment into a partitioning scheme. The advantage of using a partitioning scheme is that each subset of sites can be independently modeled, which can have a substantial impact on the results of a phylogenetic analysis. PartitionFinder currently requires that the user predefine subsets (they often choose to do so by gene or codon position). Such assignments can often be arbitrary and may not result in the best fit model. This is especially true for alignments that include several different types of data (ultra conserved elements, introns, etc.), which are becoming increasingly common. This project will expand the utility of the software by implementing a new algorithm to automatically split either user defined subsets or entire alignments into one or more new subsets using site-specific substitution rates. This new functionality will result in partitioning schemes designed to closely reflect biological processes.