HyPhy message board
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
HYPHY Package >> HyPhy feedback >> branch-specific estimates of dS
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1315498551
Message started by Alex Wong on Sep 8th, 2011 at 9:15am

Title: branch-specific estimates of dS
Post by Alex Wong on Sep 8th, 2011 at 9:15am
Hello,

I am trying to obtain branch-specific estimates of dS for an alignment. Using HYPHYMP (text menus, not GUI) I ran a GY94 model, with local parameter estimation, under the "basic analyses" option. The job seems to run fine, but the only results I get are the log likelihood, kappa, and a single tree with branch lengths - and then the program quits. Is there a way to recover the branch specific estimates of dS and omega?

Thanks very much,

Alex Wong

Title: Re: branch-specific estimates of dS
Post by Sergei on Sep 9th, 2011 at 3:22pm
Hi Alex,

Not directly from Basic Analyses. You can do it through the GUI, or by following the instructions found in sections 1.5 and 1.5.1 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

The most advanced model for estimating branch specific distributions of omega in HyPhy is referenced here Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

You can run your data through Datamonkey or offline (Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login)

Sergei

HyPhy message board » Powered by YaBB 2.5.2!
YaBB Forum Software © 2000-2024. All Rights Reserved.