tree.shared command

Commands in mothur
1

Hi,

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?

Thanks

2

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

3

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

4

Thanks for suggesting FigTree. It looks really awesome!

5

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.

6

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

7

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