Question

How to compute the average distances between groups of taxa with Mega?

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8.4 years ago

cloverchicken • 0

I have pyrosequencing data set of a nuclear gene, up to 36000 sequences. I tried to compute the average distances between groups of taxa with Mega but when I defined sequence groups, Mega stopped responding? Can anyone help?

Thank you.

mega • 5.7k views

ADD COMMENT • link 8.3 years ago by cloverchicken • 0

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Thank you so much for the help. So it seems like Mega only works with 800 sequences. We decided to prepare a python code for the calculation anyway. Have a nice day.

ADD REPLY • link 8.3 years ago by cloverchicken • 0

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Any chance you have solved this problem with a python script? I am facing the same issue now where I need to calculate an average p-distance without MEGA and am not sure how to go about it.

ADD REPLY • link 7.5 years ago by rachelrodgers12 ▴ 10

score 2 · Accepted Answer · 2016-07-28

Did you give all your sequenses to MEGA6 simultaneously?

Even for MEGA6 it too many - see this picture:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840312/figure/mst197-F1/

It's Fig.1 from this article:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840312/

I've asked your question in MEGA6 HELP:

http://imgur.com/b03eN5u

MEGA can calculate these things from picture below,

http://imgur.com/Zp6pB0L

Are you sure the mean value you need is among them?