Compare Phylogenetic Trees (Newick)

Question

[Yo_O]

hi, I'm currently working on several phylogenetic trees and I want to compare them 2 by 2. I discovered the software TreeJuxtaposer, who is an excellent software by the way, but my trees are huge and TJ is not very good with this kind of trees (in my point of view...). So I'm searching a TJ-like software for huge trees... Does anyone know a good one ?? :/

Thx a lot

[Yo_O]

i checked out before to post here... The post doesn't answer my question : I search a phylogenetic trees comparaison software :/

[Thaman]

Please check previous thread What Is A Good Phylogenetic Tree Display Program For Large Data Sets?

Answer 1

[Casey Bergman]

You can try the pairwise tree comparison method of Nye et al. (2005) which is implemented as a java applet here. It takes 2 newick trees from the same OTUs and allows you to visualize where a clade in one tree is found in the other. I'm not sure if it handles very large datasets though...

[Yo_O]

thx a lot, but I tried it too... It doesn't accept my huge trees... :(

Answer 2

[Thaman]

I believe Archaeopteryx is best suitable when dealing with huge trees. Futher, have you checked list of phylogenetic tree visualization software in the Wikipedia? From Wikipedia list you can visit individual phylo-tool link and read their documentation.

[Yo_O]

Yep, I tried a lot of softs... I found all of them here : http://evolution.genetics.washington.edu/phylip/software.html who is more complete than the wikipedia's list :)

[Thaman]

Then you have to implement them too :)

[Yo_O]

My deadline doesn't allow me to do it, it's the reason why I search an existing thing... :)