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Old 03-29-2020, 11:40 AM   #1
lnzsy
Junior Member
 
Location: California

Join Date: Mar 2020
Posts: 1
Default A newbie question about guide tree

Hi, I'm currently using MAFFT to do some multi-sequence alignment. I'm totally new to this field so please please bear with me. I just have a quick question about the output of MAFFT [1]. I feed in a fasta file to the MAFFT interface and it generates a guide tree [2].
Something like this:

((((
1_m000021
:0.00000,
4_m000022
:0.00000):0.27450,
5_m000031
:0.27450):0.02307,(
2_m000011
:0.01450,
3_m000012
:0.01450):0.28307):0.39058,
6_m000041
:0.68815);

I have no clue of what the weight represents. I know, e.g. (1_m000021:0.00000, 4_m000022:0.00000) means these two sequence has no difference. My guess was the weight represents the distance between the two children cluster. But sometimes, I see this ((...):0.0323, (...):0.1231). I thought the distance should be symmetric so I'm confused about how the weights can be different. So, exactly, what does the weight present? Is there any doc explaining this? I'm really new to this area and I'm working on some stuff by myself.

Thanks a lot!
-Shawn

[1] https://www.ebi.ac.uk/Tools/msa/mafft/
[2] https://www.ebi.ac.uk/Tools/services...&analysis=tree
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