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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl HYPHY Package >> HyPhy feedback >> Robustness towards alignment errors and INDELs for methods in HY http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1346160357 Message started by Jae on Aug 28^th, 2012 at 6:25am

Title: Robustness towards alignment errors and INDELs for methods in HY
Post by Jae on Aug 28^th, 2012 at 6:25am

Hello Developers of HYPHY

I had a general question wondering if methods such as Branchsite REL or MEME have been examined for its performance under different aligner programs?

I understand PAML and SLR have looked into this issue and I was wondering if the developers of HYPHY have similarly looked into this?

And I apologize if this has been mentioned somewhere else.

Thank you very much

Sincerely

Jae

Title: Re: Robustness towards alignment errors and INDELs for methods in HY
Post by konrad on Aug 28^th, 2012 at 2:13pm

Dear Jae,

Alignment quality is definitely important and can have a strong effect on any of these evolutionary analysis. To my knowledge, the effect has not been analyzed extensively (either by us or by the developers of PAML and SLR) beyond pointing out that it is there and that evolutionary analyses on poor alignments cannot be trusted.

The bottom line is to always inspect alignments manually and be aware that any alignment errors may cause incorrect inference of phylogeny and/or selection.

Hope this helps,
Konrad