tree.shared command


I am using tree.shared command to generate a dendrogram (OTU-based approach for beta diversity) with an as input file. Each calc option results in three files: - tree for all the 1000 iterations it did - average of the 1000 iterations - ? 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?


FigTree can accept the newick format, and has quite a few nice tools for editing/colouring/labeling as well as exporting graphics.

Could you also tell me what the ‘.cons.tre’ file is?

Thanks for suggesting FigTree. It looks really awesome!

Could you also tell me what the ‘.cons.tre’ file is?

It’s the consensus of 100 or 1000 or whatever trees that were generated by subsampling your data.

Could you explain what one means by consensus? Is it like mode/median?

This has a pretty decent illustration of what is meant by a consensus tree: