Hi Guojon, bootstrap values are what they are, and to a degree it doesn't matter how many times you bootstrap, you would (mostly) get about the same results. Low bootstrap support doesn't mean that there is something wrong with your sequences. It probably just means that they are not informative enough to support a certain node in your tree. It is possible that if you had longer sequences, more genes etc.. bootstrap values change. Hope this helps.

Hello 

While the time selection of tree construction method, option is available in message window to imporove bootstrap value.

Thank you Prashant!

Unfortunately,  I failed to find the window you told, Can you give a more detail clue?  BTW, Do you use MEGA as well ?

Yes,

The image you have pasted here, in this same image option is available where u can change the number of steps. Default it is 100, u can choose according to your data set.

Thank you Prashant,

I am sorry and actually I mean how to improve the boostrap value which will appear on the phylogenetic tree as a reuslt , not how many times to do the bootstp

Hi Guojon, bootstrap values are what they are, and to a degree it doesn't matter how many times you bootstrap, you would (mostly) get about the same results. Low bootstrap support doesn't mean that there is something wrong with your sequences. It probably just means that they are not informative enough to support a certain node in your tree. It is possible that if you had longer sequences, more genes etc.. bootstrap values change. Hope this helps.

Thank you Jimena