How to clean multiple protein sequences alignement in order to make a phylogenic three ?

Question

[GlouGlou]

Hello !

I have multiple protein sequences that i would like to align properly using MEGA and muscle algorythm . Teachers told me that in order to have a reliable three I first have to "clean" my multiple alignement by selecting the most variable regions, remove region with too many missing data,...

Can someone explain me hwo to do that exactly ?

Thanks you very much !

[gayachit]

MEGA itself has options to add, delete, trim sequences once you've aligned them. You can see the conserved and variable regions as well. Also you can refer : https://www.researchgate.net/post/Best_program_to_align_and_clean_up_sequences2

Answer 1

[Mensur Dlakic]

The goal is to increase the signal and remove the noise from alignments. In simplest terms, that means running alignment programs with their most accurate (and usually slowest) settings, and performing alignment trimming. The trimming portion can be done using trimAl and Gblocks. There are numerous MEGA tutorials on its main website and on YouTube, which is at least part of the reason why the program is so popular even though there are far more rigorous alternatives out there.