Question: How to compute the average distances between groups of taxa with Mega?
0
gravatar for cloverchicken
2.7 years ago by
cloverchicken0 wrote:

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 • 2.1k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by cloverchicken0

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 REPLYlink written 2.7 years ago by cloverchicken0

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 REPLYlink written 22 months ago by rachelrodgers120
2
gravatar for natasha.sernova
2.7 years ago by
natasha.sernova3.4k
natasha.sernova3.4k wrote:

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?

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by natasha.sernova3.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 839 users visited in the last hour