Hi Giovan,

I always use Arlewin 3.5 software to test the significance of variation between two individuals, and in turn calculation of P values and non-differentiation.

I have prepared a manual for phylogenetic studies that include all software reuired for the reason of teaching in population genetic course. so, if you interested, i can send to you,

Good luck

Farhat

Hello Giovan,

To compare if the substitution rates are different in the two gene segments, you should model the rate with two independent parameters in the two segments. Then you need to fit this model and a model where the two rates are the same -using maximum likelihood. This would allow you to do a likelihood ratio test (with 1 d.f.). If the test is significant then the rates are different.

This can be done with the PAML package (by Ziheng Yang) for a fixed phylogeny.

If you actually interested in inferring the phylogeny, you should use our program CodonPhyML (but the multi-loci version of it).

The standard version is available online:

http://sourceforge.net/projects/codonphyml/

The multi-loci version is not online yet, but if you are interested you could contact my student Stefan Zoller , he can send you a trial version.

Then you can see which model (2 rates o 1 rate fits better) and whether using 2-rate model makes a difference for the phylogeny.

Hope this helps!

Hi Giovan,

I always use Arlewin 3.5 software to test the significance of variation between two individuals, and in turn calculation of P values and non-differentiation.

I have prepared a manual for phylogenetic studies that include all software reuired for the reason of teaching in population genetic course. so, if you interested, i can send to you,

Good luck

Farhat

Farhat, can you send me these manual, please? I've been studying phylogenetic relations of fish parasites and I need more information about the news softwares fo me. Thank you so much.

Hi farhat, can you share me your software for my reseach use. I am studying phylogenetic relations in araneae families.

Best wishes

Thank you Maria Anisimova. I am gonna try to run the analyses in the PAML package and the CodonPhyML software. Farhat, I am also interested in the manual that you said; I will be very grateful with you if you can share it with me

I do not know much about it but following paper may find you useful.

African Sequence Variation Accounts for Most of the Sequence ...

www.ncbi.nlm.nih.gov › Journal List › Genetics › v.170(4); Aug 2005‎

by G Schöfl - ‎2005 - ‎Cited by 8 - ‎Related articles