How To Collapse Polytomies On A Phylogenetic Tree?

Question

[John]

A reviewer has requested that my cladogram should have the unsupported and only moderately supported relationships should be collapsed into a polytomy. This applies to only two branches of my cladogram, which I have labeled with the weak support values of 16 and 33.

However, I am having trouble collapsing the tree. I should just be able to do it manually with Adobe Illustrator, but I can't picture what it will look like collapsed, can you help? I could also do it with some software, but I'm not sure which software is best to use for this.

Answer 1

[SES]

I would first recommend FigTree which will allow you to just click the node you want to collapse and one more click on the collapse button...and it's done! MEGA probably offers the same capability and you can do this through R phylogenetics packages, but I won't go into specifics unless you need another solution.

[DG]

I highly recommend FigTree. It easily allows you to manipulate your tree and output to postscript (which you can then import into Illustrator).

[DG]

As a scientific comment BTW your reviewer is wrong. To anyone even remotely familiar with interpreting phylogenies/cladograms with bootstrap support values we already know what low or moderate support values mean in terms of the probability of a split being incorrect. If the split that is unresolved is important to the analysis it should be analysed accordingly (AUC tests of alternative topologies for instance). Otherwise collapsing it into a polytomy doesn't change the interpretation. It is entirely possible that an unsupported branch actually goes somewhere else entirely in the tree

[mccarthy.tw]

As far as I can tell, this is not how the Collapse button works in Figtree. It collapses everything above the node you select into one thing, it doesn't produce polytomies.