Phylogenetic tree - (Oct/15/2007 )
Hello everyone,
I was given a task to construct a phylogenetic tree that would measure evolutionary distances between the gene of our intrest and related genes. I decided to use MEGA 2.0 program for this. Is anyone familiar with this program?
I have retrieved amino acid sequences of the genes from GenBank and aligned them using Clustal W in the website: http://www.ebi.ac.uk/Tools/clustalw/index.html. using defaul settings. I saw that there was extra amino acids in the end of alignment (protruding ends) so I manually deleted these amino acids from each sequences and aligmed it again in Clustal W (did this because I could not find a program that could delete these amino acids from the alignment and would have been compatible with MEGA; Genedoc was not compatible). Eventually there was 387 amino acids, including gaps. Then I saved the data in aln form and send it to MEGA program and convertid into the MEGA format. I am conserned about the gaps. Is it OK that there is gaps in the alignment and in the MEGA format? Then I contructed a NJ tree (pairwise compute, bootsrap 1000). Which is the right tree in the output; original tree or Bootstrap tree, since they are different?
I would be thankful if there would be anyone that has used MEGA program and could help me. I found that the MEGA program manual was not so easy to read by a beginner.
Thanks.
Also try BioEdit and CLC free workbench. I don't know if they are any easier because I never used MEGA 2.0, but they work very well.
Hi Sarita,
What you have done are OK. The internal gaps of the sequence alignment are informative and will be calculated by MEGA to give distance matrix which will be then used to determined the branch length of each taxa. Remember to choose the correct options when a MEGA Dialog ask you to select (i.e. protein or DNA? protein coding sequence?)
You should get the bootstrap tree, not the original tree. I think MEGA is a good tool and easy to practice. The version 4 is available now.
Get it and enjoy,
Phuc V.N.