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Use of DARwin For Dendrogram Analysis

This document provides instructions for using the DARwin software to perform various analyses on genetic data, including: 1) Importing data files, calculating dissimilarities, constructing hierarchical clustering trees, and drawing trees. 2) Performing Mantel tests to assess goodness of fit between trees and dissimilarity data. 3) Conducting principal coordinate analyses (PCoA) to ordinate individuals based on dissimilarity matrices. 4) Performing bootstrapping analyses to assess support for clusters in trees.

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Corbeau Le
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335 views2 pages

Use of DARwin For Dendrogram Analysis

This document provides instructions for using the DARwin software to perform various analyses on genetic data, including: 1) Importing data files, calculating dissimilarities, constructing hierarchical clustering trees, and drawing trees. 2) Performing Mantel tests to assess goodness of fit between trees and dissimilarity data. 3) Conducting principal coordinate analyses (PCoA) to ordinate individuals based on dissimilarity matrices. 4) Performing bootstrapping analyses to assess support for clusters in trees.

Uploaded by

Corbeau Le
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Use of DARwin for dendrogram analysis

File format:
DARwin uses tab delimited text files. You can make sure files in Excel and then
Save As: tab delimited text
See example file for other formatting features

Using the program:

Open DARwin
Under ‘File’ select ‘import data matrix’ & select file ‘srap-ssrdata.txt’
In window, click ‘Save file as.’ (The program uses the original file name as the default name.
This is fine, no need to change it.)
Click on Save in next window.
Change ‘Integer code for missing data’ to 9.
Click ‘OK.’ You should see a completed procedure window. Close this window.
Under ‘Dissimilarity’ click ‘Calculate from single data.’
In new window ‘Open’ the file that you just saved.
In ‘Calculate dissimilarities from single data’ window, click ‘Save dissimilarity as…’ and use
default name.
Under ‘Missing data’ click on ‘Options’ and check ‘Some data are missing.’
Change ‘Integer code’ to 9.
For ‘pairwise variable deletion’ select ‘50%’.
The rest of this window’s variables do not need to be changed for our analysis.
Click ‘OK.’ Again a window should appear indicating procedure is completed. Close
window.
Under ‘Tree construction’ select ‘Hierarchical clustering.’
In new window, ‘Open’ the dissimilarity file (.dis) that you just made.
‘Save tree as’ using default name.
Select ‘UPGMA.’
Click ‘OK.’ Again a window should appear indicating procedure is completed. Close
window.
Under ‘Trees’ select ‘Draw.’ Choose tree (.arb) file that you just made. A tree will appear.
Play with the type of tree using the icon called ‘Tree representation.’
Play with the labeling of the tree using icon called ‘Identification and illustration.’
Click on ‘Identifiers’ in the drop-down menu to select the appropriate file (.don)
which will allow you to use your own accession names. Then click on down arrow
next to ‘Identifiers’ to select ‘No’ instead of ‘Unit.’

Repeat procedure using ‘Unweighted neighbor joining’ under ‘Tree construction’ to draw a
NJ tree.
For a Mantel test:

Under ‘Trees…’ choose ‘Fit Criterion.’ Select the tree file that you just made (it will have a
‘.arb’ extension. By default, the program will compare your selected tree file with its
corresponding dissimilarity file.
Click ‘ok.’
The window that opens gives you the Mantel test correlation as the cophenetic r
value. This value indicates the goodness of fit between your tree and the
dissimilarity data.
r > 0.9 very good fit
r > 0.8 good fit
r = 0.7-0.8 poor fit

For principal coordinate analysis (PCoA):

Under ‘Factorial Analysis’ choose ‘Analysis.’


Open your dissimilarity file (.dis).
‘Save coordinates as’ using the default name.
Click ‘ok.’
Two windows will appear.
The first window will show your individuals graphed on the first 2 coordinates. You
may change these using the ‘Select axes’ icon on the toolbar.
The second window will give you the Eigen vectors and their values.

For bootstraps:

In the ‘Dissimilarity’ window, change ‘Number of bootstraps’ to 1,000 or more.


When constructing tree, click ‘Bootstrap analysis’ box in bottom left corner.
After drawing tree, you can choose to hide or display bootstraps using the drop-down tools.

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