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Compare Phylogenetic Trees (Newick)

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

phylogenetics tree visualization comparison
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updated by Biostar Biostar • written by Yo_O • Yo_O

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

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written by Yo_O • Yo_O

2 answers

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...

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written by Casey Bergman Casey Bergman

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

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written by Yo_O • Yo_O

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.

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written by Thaman Thaman

Then you have to implement them too :)

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written by Thaman Thaman

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

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written by Yo_O • Yo_O

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