The R package 'Ape' has some functions to compare trees and also plot two trees next to each other. For example the function 'all.equal.phylo'

See the manual here: http://cran.r-project.org/web/packages/ape/ape.pdf

Mesquite works great in general and should for your cause as well. Additionally, it is open source and is generally well accepted by reviewers.

http://mesquiteproject.org/mesquite/mesquite.html

The R package 'Ape' has some functions to compare trees and also plot two trees next to each other. For example the function 'all.equal.phylo'

See the manual here: http://cran.r-project.org/web/packages/ape/ape.pdf

You could also use Splitstree, with your 2 trees as input, it would draw a network for both and you could easily see where you have discrepancies.

http://splitstree.org/

All of the options presented here will work.

I like splitstree because it is easier to implement than the Ape package in R and produces better graphical representations than Mesquite.

I hope that helps!

Another method in R is the Distory package. It has a range of functions for comparing two trees. It is probably not as good visually as Splitstree (though it does have a function to visually show both trees and highlight the differences), but if you want to do further analysis on the differences then it can be quite powerful. Here are a couple of useful functions:

1. phylo.diff plots two trees side by side, highlighting edges unique to each tree in red.

2. distinct.edges finds the edges present in the first argument not in the second.

3. dist.multiPhylo Computes the geodesic distance of a list of phylogenetic trees using a polynomial algorithm.

There is also TOPD/FMTS, a programme for comparing phylogenetic trees. The software implements several described methods for comparing phylogenetic trees and calculating the "TOPological Distance" between them.

http://genomes.urv.cat/topd/

may be this will help you

http://www.plosntds.org/article/info%3Adoi%2F10.1371%2Fjournal.pntd.0002738

Have a look at Compare2Trees (http://www.mas.ncl.ac.uk/~ntmwn/compare2trees/index.html).

Nicolas, Weston. I wonder how do I compare two trees in SplitsTree4 ? I tried everything but could not figure it out, and a manual says nothing about tree comparison. Could you please give me an advice?

Janos Podani's Syn-Tax 2000 package (https://www.exetersoftware.com/cat/syntax/syntax.html; http://ramet.elte.hu/~podani/) implements methods for comparing two or more trees, as described here: Podani, J., and Dickinson, T.A. 1984. Comparison of dendrograms: a multivariate approach. Canadian Journal of Botany 62(12): 2765-2778. See also Podani, J. 2000. Simulation of random dendrograms and comparison tests: some comments. J. Classif. 17:123-142 and Podani, J., A. Engloner and A. Major. 2009. Multilevel comparison of dendrograms: A new method with an application for genetic classifications. Statistical Applications in Genetics and Molecular Biology 8(1): Article 22. DOI: 10.2202/1544-6115.1443. 

Go to CRAN, phylogenetics task view and under the subsection called tree comparison you will find a list of R packages that do tree comparison, here is the copy paste of that paragraph :

Tree Comparison: Tree-tree distances can be evaluated, and used in additional analyses, in distory and Rphylip. ape can compute tree-tree distances and also create a plot showing two trees with links between associated tips. kdetrees implements a non-parametric method for identifying potential outlying observations in a collection of phylogenetic trees, which could represent inference problems or processes such as horizontal gene transfer. dendextend can evaluate multiple measures comparing dendrograms.

You could also use TOPD/FMTS: a new software to compare phylogenetic trees

http://bioinformatics.oxfordjournals.org/content/23/12/1556.full

Consider https://cran.r-project.org/web/packages/nLTT/

People interested in tree comparisons might be interested in this:

Podani J, Dickinson TA (1984) Comparison of dendrograms: a multivariate approach. Canadian Journal of Botany 62: 2765-2778.

Podani's more recent work can be seen at http://ramet.elte.hu/~podani/subindex.html

Take a look at Fig. 2.6 : https://yulab-smu.github.io/treedata-book/chapter2.html

Or something like this in R:

library(ggtree)

# create random trees

firstTree

One of the easiest ways I've run to is web based and interactive http://phylo.io/ . All you need is two trees in newick format.

All best

Another R package for this purpose is treespace. its related tree functions (concordance, distance) can be especially useful.

https://cran.r-project.org/web/packages/treespace/vignettes/tipCategories.html

https://cran.r-project.org/web/packages/treespace/vignettes/introduction.html

and a web interface!

http://shiny.imperial-stats-experimental.co.uk/users/mlkendal/treespace/

treespace: Authors / Contributors

Authors:

• Thibaut Jombart
• Michelle Kendall

Contributors:

• Jacob Almagro-Garcia
• Caroline Colijn

Maintainer of the CRAN version:

• Michelle Kendall

If you just want to get an overall picture on how much difference between the two trees, 'comparePhylo' function from R, ape package can compare two trees side by side and highlight the clades that are different between two trees. It required exact node label for both trees though.