I don't have any batch file for PAUP to create Maximum Likelihood tree. I looked so many places but I couldn't find any. Please help me.
Hi Ortac
I have some files, send me your email address. I will send them to you.
Best,
Ahmad
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
Luc Legal, I followed your steps but can not generate the tree.
How do I insert the model?
My matrix is concatenated are two genes, both resulted GTR+I+G, but the values are different.
./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;
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