mothur

What is the "tree.sum" file?

I’m a newcomer to Mothur. Recently I have worked with Mothur packages on Galaxy and noticed that “classify.seqs” command outputs, in addition to the results, “tree.sum” file. Can anybody explain to me what exactly is this file, how to read its columns and why it is created?

The .tree.sum file is a shortcut file mothur uses to represent reference file’s taxonomy. It reduces processing time. It is not an output file for the user. Here’s what the lines represent:

#versionOfMothur
numberOfTreeNodes
maxDepthOfClassifications

for each node mothur outputs info:

nodeLevel numberOfChildren
nodeName
node’sChildIndex childsName

for example:

#1.44.0
6263
6
0 5
Root
2 Archaea
7 Bacteria
994 Eukaryota
2790 unclassified
1 unknown

Version 1.44.0, 6263 nodes, max classification level is 6.

The root node has 5 children: Archaea, Bacteria, Eukaryota, unclassified and unknown.

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Thank you! I’m surprised that there is no mentioning of this anywhere…