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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> branch estimates of dn/ds w confidence intervals http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1351587817 Message started by Pär on Oct 30^th, 2012 at 2:03am

Title: branch estimates of dn/ds w confidence intervals
Post by Pär on Oct 30^th, 2012 at 2:03am

I want obtain simple dn/ds estimates on branches to explore differences in purifying selection. I previously used the method that was in the handbook to obtain the confidence intervals (I understand the limitations), but the script was recently removed from your server. Are there better ways of doing this? In HYPHY, I can obtain confidence estimates on dN and dS separately, but not I believe for the ratio. Some pointing in the right direction here would be highly appreciated!

Title: Re: branch estimates of dn/ds w confidence intervals
Post by Sergei on Oct 30^th, 2012 at 12:27pm

Hi there,

I've repaired the issue with missing server files: thanks for alerting me to this issue.
You can look at the source code of Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Login to get an idea of how the errors are estimated in HyPhy; please post follow-up questions if you need further guidance.

Sergei