Hi Ortac

I have some files, send me your email address. I will send them to you.

Best,

Ahmad

I send my mail to you.

at this point, I'd use RAXML instead of paup.  it is very easy to use

PhyML will be useful too

If PAUP is critical, there are several examples of how to specify ML in the manual  

http://paup.csit.fsu.edu/Cmd_ref_v2.pdf

New PAUP* (test version): http://people.sc.fsu.edu/~dswofford/paup_test/

please tell be if you are using a Mac or a PC?

Alternatively to Paup which is highly time consuming but still...the best software to perform ML analysis....you may use Garli.

On a PC

after loading your dataset

set cr=l

lset sha=e pi=e rm=e ra=g ns=6

hs addseq=random

This if you want to apply a GTR + G + I model

If your data set is big you may run a fast search in parsimony or NJ save tree and then

instead of the last line run

hs start=1

Hoping it helps

Cheers from Luc

Thanks Luc. I use PC.

Luc Legal, I followed your steps but can not generate the tree.

Thais

Sure? check well what you entered as these commands are correct.

Tell me if you manage to succeed or contact me.

Cheers from Luc

How do I insert the model?

My matrix is concatenated are two genes, both resulted GTR+I+G, but the values are different.

The values of what ????

Modeltest ???

I sent a message to you explaining. Thanks for help me

./paup4a164

log start file=ML.log;

exec your_alignment.nexus;

dset distance=logdet;

automodel;

set criterion=likelihood;

hsearch;

describe/plot=p;

savetrees file=ML.tre;