Hello,

My sequences have 0.1%-2.5% diversity, is this too low to use SBP and GARD?  Other recombination tools say you need a minimum diversity (~5%).  I've noticed others publishing using GARD with similar data to mine though, and in the paper about these methods there were some low diversity alignments included, so I decided to give it a try!

I ran sequences from the person with the highest diversity and SBP resulted in Yes for recombination (cAIC 4.25 improvement, 89.7% support), then the GARD said no recomb (used the model selection tool and 4 rate categories).  I'm very new at this, is it normal for the 2 to disagree?  My plan was to use SBP to determine if there is recombination, then follow-up with GARD to find the breakpoints.  Are the differences in my alignments too few to expect findings of recombination?  I did notice in table 1 of  the paper where delta was <100 there were no breakpoints.

The sequences are ~1000 bp and ~15 per alignment.

Thank you!
Liz  

Hi Sergei,

Thank you!  I have one additional question (for now!!).  I read some of the other posts, and am trying to use HyPhy GARDProcessor.bf

I uploaded my alignment, and the [CSV] output from GARD.  It's been running on my (old) computer for 3 days, and it's still fitting the single tree (currently tree_300).  Did I do something wrong, is is caught in a strange loop, or is it just my horribly slow computer? 

I know this is slightly off-topic, but if I need to seek out a faster computer I figure it's best to find out sooner, I've got a couple of these to do, and a deadline  .
Thank you,
Liz

Thank you!  I was pretty confused as to why there was a KH report at the bottom of GARD if we had to run it separately, but I'm still at the following directions stage, trying to move into actual understanding!!

Liz