How can i calculate bootstrap by Mega ??

Question

[eng_samar_zayed]

I need to know how to calculate bootstrap by Mega in steps please

and what is my input and my output??

[sridhar56]

I am not sure I understand your question here! You usually set the number of bootstraps while running a phylogeny and not the other way round.

Let us know what you are trying to achieve for us to help you further.

[eng_samar_zayed]

I have tree topology constructed from distance matrix and i need to calculate bootstrap for it .

i can't find this option when i construct my tree by distance based method (NJ algorithm).

[sridhar56]

Lets assume you have an multiple sequence alignment file either in the .meg format or a fasta file, when you click on phylogeny and choose the construct/test tree, I would choose maximum likelihood, but you can choose the NJ method:

You get the window, Analysis preferences where you can set the bootstrap method under the test of phylogeny and set the number of bootstraps you want to set. (I usually set 100 which is a good enough number, if you want you can set 500 or even 1000 as this number).

I hope this helps. If this is not what you are looking for, let me know what you are trying to achieve by a Bootstrap test.

[eng_samar_zayed]

I need to compare between 2 tree files or 2 distance matrices that constructed these tree one of them generated from new and trusted software as you previously indicated and the other i have constructed its distance matrix and optimized it by optimization algorithm , then i need strong metric for comparison between them to indicate that my method (my construction distance method) achieve better results than that constructed by Mega. Is bootstrap enough ?? or it is not my suitable metric ?? Also what can i use to compare between distance matrices or tree files ??

[sridhar56]

I think you can do that by using the treedist function in phylip to compare your trees. You can take a look at this link and see if it helps you.

Tree dist function in Phylip

[eng_samar_zayed]

i need another separate metric like bootstrap that not depend on relationship between trees ..... i hope to understand me .. i really need help in this part .

[eng_samar_zayed]

please,if i have my distance matrix constructed from free alignment method ... Can i calculate bootstrap for specific distance matrix ??

[hashish]

Thank you so much for posting I was searching

Answer 1

[mihawxxzoro]

I was searching for an answer to the same question but then figured it out . This is 2 years later but I hope its still relevant to anyone searching for the same inquiry. I'm currently using the latest version of Mega which is Mega-X. So if you want to calculate bootstrap using a Neighbour-Joining Phylogeny Test, you first click on the Neighbour-Joining Phylogeny Test, select your multiple sequence alignment file and then a settings menu will pop-up. In the settings menu, look for PHYLOGENY TEST, under it you will see Test of Phylogeny -> none. Click on none and change it to bootstrap method and set your desired number of replications and then run the test!