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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> testing for dated taxa bias http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1317834149 Message started by rbjmax on Oct 5^th, 2011 at 10:02am

Title: testing for dated taxa bias
Post by rbjmax on Oct 5^th, 2011 at 10:02am

I want to determine if the dates of my taxa are affecting the evolutionary rate, etc., in a biased manner. I would like to calculate a root-to-tip distance vs sample date regression analysis, using a tree file. Can this be done in HyPhy?

thank you!
Rachel

Title: Re: testing for dated taxa bias
Post by Sergei on Oct 7^th, 2011 at 11:51am

Hi Rachel,

It can be done in HyPhy (e.g. the DatedTipMolecularClock.bf analysis uses a linear regression to estimate ages on internal nodes), but I would recommend you use a specialized (and very user-friendly) program written for this exact purpose by Andrew Rambaut: Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to

Title: Re: testing for dated taxa bias
Post by rbjmax on Oct 11^th, 2011 at 11:39am

thanks for reminding me of that program, I had completely forgotten about it.
Rachel