How to compute the average distances between groups of taxa with Mega?
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.
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cloverchicken •
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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:
MEGA can calculate these things from picture below,
Are you sure the mean value you need is among them?
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natasha.sernova
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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.
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.