Hi Ana,
Regarding the large GARD analysis, there are several things you can do.
1). If you send me the alignment, I could run it through GARD on the cluster without a time limit.
2). You could use the preliminary GARD results (I assume it is showing some evidence of recombination), to partition the alignment by sites, i.e. if GARD finds 1 breakpoint, you can independently run the section left of it, and then the one right of it.
3). You could randomly split your data set by sequences (e.g. 1/2 or 1/4 of sequences) and run all of them through to see if the results are consistent between splits. If they are not, then the likely cause is that one or more of the sequences present in one part of the data set but not in others are driving recombination signal.
In terms of correcting selection analyses, you should select 'GARD Trees' from the
Use this tree set option list. You could see whether recombination is affecting results by comparing the results of a single partition analysis, vs the GARD-inferred set analysis. Take a look at the first exercise in Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
for an example.
Sergei
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