hotgroup

"Hotgroup" is a small perl script that randomizes outgroup combinations for phylogenetic analyses. It may be useful for you if would like to know how sensitive your tree rooting is to different outgroup combinations (both the identity and the number of outgroups). It accepts three inputs: the number of outgroups in your analysis, the number of outgroup jackknife replications you would like to generate, and the name of the nexus file that contains the paup block (including your data matrix) that will run your subsequent analyses. If you want to control how many outgroups are selected (i.e., "always use two outgroups"), that is a fourth optional argument. Hotgroup will generate a nexus file called "hotgroup.nex" that will contain all jackknife replications with your original nexus file embedded within each of them. NOTE: for this to work, your outgroups MUST be the first taxa in your data matrix. This has only been tested in OSX, but it should work on other platforms as well. Written with Casey Dunn.