Question: Compare Phylogenetic Trees (Newick)
3
gravatar for Yo_O
8.6 years ago by
Yo_O130
Yo_O130 wrote:

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

ADD COMMENTlink modified 5.8 years ago by Biostar ♦♦ 20 • written 8.6 years ago by Yo_O130
1

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

ADD REPLYlink written 8.5 years ago by Yo_O130

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

ADD REPLYlink modified 28 days ago by RamRS24k • written 8.5 years ago by Thaman3.2k
2
gravatar for Casey Bergman
8.5 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

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...

ADD COMMENTlink written 8.5 years ago by Casey Bergman18k

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

ADD REPLYlink written 8.5 years ago by Yo_O130
1
gravatar for Thaman
8.5 years ago by
Thaman3.2k
Finland
Thaman3.2k wrote:

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.

ADD COMMENTlink written 8.5 years ago by Thaman3.2k

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 :)

ADD REPLYlink written 8.5 years ago by Yo_O130

Then you have to implement them too :)

ADD REPLYlink written 8.5 years ago by Thaman3.2k

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

ADD REPLYlink written 8.5 years ago by Yo_O130
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