search

husonlab / dendroscope3

Dendroscope program for analyzing and visualizing rooted phylogenetic trees and networks
GNU General Public License v3.0
42 stars 5 forks source link

How to compare two trees topologies. #15

Open limin321 opened 4 years ago

limin321 commented 4 years ago

Hi

I want to compare two phylogenetic trees topologies using dendroscope. In the user-manual, the "Algorithms" option is used for topologies comparison. however, there is no details how to do this comparison.

Could anyone please tell me the steps they take how to do this comparison? I am able to open two trees in dendroscope, and root them. Then I don't know how to compare them.

Your help will be greatly appreciated. Best,

husonlab commented 4 years ago

Both trees need to be in the same document And both visible Either open one and then use the Add menu item to add the second or open both separately and then copy and paste the second into the first You then need to set the visualisation grid to 1x2 or 2x1 to see both trees (Using the toolbar item that looks like a grid) Then the tanglegram menu item will be enabled Daniel

Sent from Daniel Huson's phone

On 25 Jul 2020, at 04:36, limin notifications@github.com wrote:

 Hi

I want to compare two phylogenetic trees topologies using dendroscope. In the user-manual, the "Algorithms" option is used for topologies comparison. however, there is no details how to do this comparison.

Could anyone please tell me the steps they take how to do this comparison? I am able to open two trees in dendroscope, and root them. Then I don't know how to compare them.

Your help will be greatly appreciated. Best,

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

limin321 commented 4 years ago

Both trees need to be in the same document And both visible Either open one and then use the Add menu item to add the second or open both separately and then copy and paste the second into the first You then need to set the visualisation grid to 1x2 or 2x1 to see both trees (Using the toolbar item that looks like a grid) Then the tanglegram menu item will be enabled Daniel Sent from Daniel Huson's phone … On 25 Jul 2020, at 04:36, limin @.***> wrote:  Hi I want to compare two phylogenetic trees topologies using dendroscope. In the user-manual, the "Algorithms" option is used for topologies comparison. however, there is no details how to do this comparison. Could anyone please tell me the steps they take how to do this comparison? I am able to open two trees in dendroscope, and root them. Then I don't know how to compare them. Your help will be greatly appreciated. Best, — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

Hi Daniel. Thank you so much. It works now. I copied two trees in text file, and saved it as .tre file. Then I open this in dendroscope, automatically two trees show up in the screen. The Algorithms - Tanglegram is amazing to compare the two trees.

By the way, do you have any suggestions where I can learn more details about Algorithms option. The manual itself is not enough for me to understand them, I am a beginner on phylogeny studies.

Really appreciate all your help. Save me great time for tree comparison. Best, Limin

limin321 commented 4 years ago

By the way, I am going to compare a lot of gene trees with species tree(which is constructed from all core genes) to see which gene tree can be used as species tree. If there are any python codes which I can do the same comparison, otherwise, I will have to compare the trees hundreds of times.

Thanks a lot. LImin