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Bootstrapping In Clustalw

I've a set of nucleotide sequences and I used clustalw v.2.1 to align those sequences. The next thing I did was to generate a tree using the .dnd file in a Tree visualization software. I incorporated a -BOOTSTRAP function in the clustalw but the tree did not display the bootstrap value. I even checked the .dnd file with only listed the distance value but not the bootstrap value.

The command I used in the perl script for clustalw alignment was

system("$clustalw -INFILE=$in_file  -OUTFILE=$out_file -TYPE=DNA -CLUSTERING=NJ -BOOTSTRAP=1000 -CONVERT=Phylip");

How can I display the bootstrap values in the tree? Is anything missing in my command? I did not get a clear explanation on it in the clustaw help file!!

clustalw tree
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updated by Gustavo Gustavo • written by raunakms raunakms

What software are you using to view the tree? There may be an option to show/hide the bootstrap values, or to place them at nodes/leaves.

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written by Neilfws Neilfws

I'm using FigTree (http://tree.bio.ed.ac.uk/software/figtree/) to visualize the Tree. There is an option in FigTree to display branch length or its values. But the original .dnd file itself does not contain any bootstrap values !!!

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written by raunakms raunakms

1 answer

The .dnd file isn't a phylogenetic tree (even though it has a similar format): it is a "guide tree" for the alignment stage.

When you use the clustalw option to create a phylogenetic tree with bootstrap, select phylip output format. The bootstrap values will be included in the phylip output.

(Edited to add: I see you already indicated phylip output. See if the run produced a separate .phy file for this, not the .dnd file.)

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written by Gustavo Gustavo

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