Dear Albert,

I have added the save option to save trees to a file inside 'syn and non-syn trees'. Drop this file [url] http://www.hyphy.org/pubs/post_sns.bf [/url] into TemplateBatchFiles to enable the changes.

So, a console sequence would look like this:

       Available Result Processing Tools
        ---------------------------------


       (1):View Results
       (2):Save Results
       (3):Variance Estimates
       (4):Save Covariance Matrix
       (5):Parametric Bootstrap
       (6):Nonparametric Bootstrap
       (7):Parameter Sampler
       (8):dN-dS for Branches
       (9):Syn and non-syn trees
       (10):Ancestral Sequences
       (11):Suzuki-Gojobori Derived Adapative Selection Tool

Please type in the abbreviation for the tool you want to use (or press q to exit):

Enter 9

                      +--------------+
                       |Output options|
                       +--------------+


       (1):Display trees on the console (and graphically if GUI is present).
       (2):Save tree strings to a file (syn followed by non-syn)

Please choose an option (or press q to cancel selection):

Enter 2
Enter file name

Resulting file will contain two Newick strings (one on each line), synonymous tree first.

E.g.

[tt]
(a:0.0363562,b:0.0706921,og:0.151923)
(a:0.0424903,b:0.0178832,og:0.0576002)
[/tt]

Cheers,
Sergei