I would like to make pairwise comparisons of topological similarity between
all possible combinations of 518 gene trees.
The expected output would be a matrix of topological distances for each
gene tree to each other tree.
Any suggestions?
Also as an aside, is there a way to mechanize the
You may use dist.topo from the ape package, there are a couple of tree
distance functions implemented.
2014-04-14 13:13 GMT+01:00 Chris Buddenhagen cbuddenha...@gmail.com:
I would like to make pairwise comparisons of topological similarity between
all possible combinations of 518 gene trees.
Hello Chris,
I know there's a program that was specifically developed for calculating
large pairwise Robinson-Foulds distances matrices efficiently. I'll be able
to send you the reference this evening (Paris time).
All the best,
E.
On 14 Apr 2014 14:44, Chris Buddenhagen cbuddenha...@gmail.com
Hi Chris.
For part (1) if you want Robinson-Foulds distance (aka. symmetric
distance) you could use multiRF in phytools
(http://blog.phytools.org/2013/09/getting-robinson-foulds-distances-for.html)
or RF.dist in phangorn, which I believe can now handle multiple trees
is probably
Hello all,
Another implementation of RF distances and others that I found easy to use is:
Bogdanowicz, D., Giaro, K., Wróbel, B. (2012). TreeCmp: Comparison of trees
in polynomial time. Evolutionary Bioinformatics Online, 8, 475.
Best,
Eduardo
On Apr 14, 2014, at 1:30 PM, Eduardo Ascarrunz
