HyPhy message board | |
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl
HYPHY Package >> Feature Additions >> More models? http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1234274983 Message started by Alan on Feb 10th, 2009 at 6:09am |
Title: More models? Post by Alan on Feb 10th, 2009 at 6:09am
For those of us who are either intimidated by the exigencies of designing substitution models in HyPhy or just feel incompetent, is there any chance that the number of available models could be increased to parallel those available in, let's say ModelTest?
Thanks. |
Title: Re: More models? Post by Alan on Feb 10th, 2009 at 8:13am
Dear Sergei,
Yes, I am "looking to simply have more predefined models in the drop down menu in the data panel interface." Best, Alan |
Title: Re: More models? Post by Sergei on Feb 10th, 2009 at 8:46am
Dear Alan,
Right. I wish I had more time... :( Can you list the models you most would like to see? ModelTest has 8 rate matrices (JC69, HKY85, TrN93 etc), the other model options are base frequencies and site to site rate variation -- you can stack those on top of the basic rate matrix to generate HKY85+G+I for example. Cheers, Sergei |
Title: Re: More models? Post by Alan on Feb 10th, 2009 at 9:05am
Dear Sergei,
I understand. I feel a bit churlish asking authors of useful, free software to do more work at my behest! As a newcomer to HyPhy, I am not yet in the comfort zone in programming alternative subst. models. SYM, TIM, and TVM would be nice, but I can also accept that I need to gird my loins and develop the parameter files for them myself. In the custom mode, can one just input the numerical substitution code? If it is as easy as that (plus specifying rates and base frequencies), I guess I shouldn't have even asked the question. Best, Alan |
Title: Re: More models? Post by Sergei on Feb 10th, 2009 at 3:07pm
Hi Alan,
Try running AnalyzeNucProtData.bf (Standard Analyses->Basic Analyses) on an alignment. When prompted for the model, select 'CUSTOM' then enter the six character model code, select Global if you want no rate variation and Global w/variation for further options (like G or G+I), rate parameters (estimated or fixed) and base frequencies (observed, equal or custom). That should cover all the bases:) The CUSTOM model should be available for all nucleotide data analyses accessible via the Standard Analysis route. Cheers, Sergei |
HyPhy message board » Powered by YaBB 2.5.2! YaBB Forum Software © 2000-2024. All Rights Reserved. |