I built a tree after removing redundant sequences, but now can’t seem to get the “names” file to work with the “read.tree” option. Do I need to include all identical sequences in my tree?
yes. i’m not sure when we’ll add a names file feature to the hypothesis testing methods. gigantic trees requiring the names deconvolution don’t exactly have reliable topologies and at some point you have so much power that you can detect the minutest of differences. this feature is on the list, but i’m not sure when we’ll get to it.