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The tree.shared command will generate a newick-formatted tree file that describes the dissimilarity (1-similarity) among multiple groups. Groups are clustered using the UPGMA algorithm using the distance between communities as calculated using any of the calculators describing the similarity in community membership or structure. Dissimilarity is calculated as one minus the similarity. This tutorial uses the data files in AbRecovery.zip.
Using the antibiotic recover data do the following:
mothur > cluster(phylip=abrecovery.dist, cutoff=0.10) mothur > make.shared(list=abrecovery.fn.list, group=abrecovery.groups, label=0.03) mothur > tree.shared(shared=abrecovery.fn.shared)
This will generate newick-formatted file for the classical Jaccard and Yue & Clayton theta values. The tree can be visualized in a number of programs such as TreeViewX. The output files are as follows:
Using the calc option allows one to select any of the calculators of similarity of community membership and structure. The different calculators can be separated with hyphens (i.e. "-"). For example the following command will generate distance matrices for the Jaccard coefficient using richness estimators, the Yue & Clayton theta, and the Bray-Curtis index:
mothur > tree.shared(shared=abrecovery.fn.shared, calc=jest-thetayc-braycurtis)
Keep in mind that these are distances, which are calculated as one minus the similarity value.
Raw Distance Matrix
To read in a phylip-formatted distance matrix you need to use the phylip option:
mothur > dist.shared(shared=abrecovery.fn.shared, label=0.10) mothur > tree.shared(phylip=abrecovery.fn.jclass.0.10.lt.dist)
column & name or count
mothur > tree.shared(column=..., name=...)
mothur > tree.shared(column=..., count=...)
At this point, if you run the following command:
mothur > get.group()
You would have seen that there were 3 groups here: A, B, and C. If you just want the distances between groups A and B, A and C, or B and C enter the following (this is an admittedly silly example):
mothur > tree.shared(shared=abrecovery.fn.shared, groups=A-B) mothur > tree.shared(shared=abrecovery.fn.shared, groups=A-C) mothur > tree.shared(shared=abrecovery.fn.shared, groups=B-C)
Keep in mind that these will output to files with the same name. So, it is important to change the file name between commands. The following reverts to the default behavior:
mothur > tree.shared(shared=abrecovery.fn.shared, groups=all)
This is the same as:
mothur > tree.shared(shared=abrecovery.fn.shared, groups=A-B-C)
There may only be a couple of lines in your OTU data that you are interested in summarizing. There are two options. You could: (i) manually delete the lines you aren't interested in from you rabund, sabund, list, or shared file; (ii) or use the label option. If you only want to read in the data for the lines labeled unique, 0.03, 0.05 and 0.10 you would enter:
mothur > tree.shared(shared=abrecovery.fn.shared, label=unique-0.03-0.05-0.10)
The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.
The iters parameter allows you to choose the number of times you would like to run the subsample. Default=1000.
The processors option enables you to accelerate the alignment by using multiple processors. Default processors=Autodetect number of available processors and use all available.
The withreplacement parameter allows you to indicate you want to subsample your data allowing for the same read to be included multiple times. Default=f.
- 1.28.0 Added count parameter
- 1.29.0 added subsampling parameters
- 1.29.0 Bug Fix: - if shared file was not in alphabetical order. All shared files created by make.shared after 6/10 are sorted.
- 1.29.2 Bug Fix: - subsampling with eliminated groups caused crashes.
- 1.40.0 - Speed and memory improvements for shared files. #357 , #347
- 1.40.0 - Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.
- 1.40.0 - Fixes segfault error for commands that use subsampling. #357 , #347
- 1.41.0 - Fixes results with shared file. #535
- 1.42.0 - Adds withreplacement parameter to sub.sample command. #262