Hi!

I am attempting to run a 2-way FEL and a SLAC analysis from the HyPhy console using QuickSelectionDetection.bf. When I run both first of all I am asked at one point for "Branch Corrections Factor (<0 to estimate). I have absolutely no idea what this is and cannot find any mention of this value in the phylogenetic handbook or online - can somebody explain this please? At the moment I am just pressing return and skipping over this.

Also, and more importantly, when I run the 2-rate FEL I get this error message:

"Operation 'MAccess' is not implemented /defined for a Number Current Task has been terminated."  

Despite Googling this I cannot find any information as to what this means or what the error is!

Can somebody please help?

Thanks!

Caz

Hi Caz,

I'll see what is causing the error. You should not, generally, be using the option that prompts you for the branch correction factor, i.e. "Neutral" or "User" for the "dN/dS bias parameter options" dialog.

Probably the best reference on using SLAC and FEL can be found in section 2 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login

The chapter explains all the relevant options and suggests which ones to use.

Sergei

Thanks Sergei! I appreciate the assistance :-) Any help with the 2-way FEL error would be great as well as I am currently running it on datamonkey and would really like to have the results from the HyPhy console as well to compare (you seem to get a few more input options on the console).

I am running it in Windows Vista (oh, maybe I've just found what the problem is right there!) :-D

Thanks again,

Caz

Hello!

I thought I would report back...I just ran the 2-rate FEL analysis, selecting "Estimate dN/dS only" instead of the "user defined" dN/dS and it ran perfectly so problem solved!

Thank you for taking the time :-)

Caz

Hi Caz,

Sure, no problem.

Let me know if you run into other errors.

Sergei