I am using tree.shared command to generate a dendrogram (OTU-based approach for beta diversity) with final.an.shared an as input file. Each calc option results in three files:
final.an.thetayc.0.03.all.tre - tree for all the 1000 iterations it did
final.an.thetayc.0.03.ave.tre - average of the 1000 iterations
final.an.thetayc.0.03.cons.tre - ? I unsure what this does.
Also, apart from just viewing the .tre file with Treeview X, Can I edit it using a different software? I came across Java Treeview, but it only accepts .cdt and .pcl formats (tab limited). Is there a way in mothur I could change the format of tree file?