ABSTRACT
Genomic data at the population and phylogenetic level either from whole genome sequencing, RAD markers, or other targeted genome reduction methods can be used in a wide variety of analysis programs. There are programs for the conversion of formats for population genomics programs that can be used to convert back and forth between programs. Partitioning simply means setting up boundaries amongst the sequences in a phylogenomic matrix. A partition’s boundaries can be based on any biologically meaningful definition. The most common partitions are defined by gene boundaries. Partitioning can be accomplished with commands specific to the program described in this chapter. Other ways of editing a large phylogenomic matrix are to use existing matrix-editing programs like Mesquite or MEGA. There are programs that exist that will take raw sequences and construct matrices automatically.
