I'm using IMa2 to get some measures of splitting times, theta and migration rates among penguin populations. I'm new to IMa2 and I'm asking around to see if someone more familiar with this analysis would be willing to take a quick look at my output to see if there is anything glaringly out of order and maybe walk me through the results a little? It will of course earn you a place in the acknowledgements! Thanks in advance.
hi, I might could have a look of it. Please contact me through the email [email protected]
Thank you Jie Gao. I will try a longer run. If you have any suggestions for improving the convergence it would be appreciated. Maybe increasing the number of heated chains would help? I may ask your opinion on my next round of results also if you don't mind? Thanks.
You are welcome! Yes, more chains are better. And it is difficult to estimate how long the burn -in steps are needed. You could try another way, set up the -b value in a floating point number (e.g. -b 12.0) then it will give you a report of the trend plots every 12 hours. You could stop the burn-in step by remove the " IMburn" file from your working folder untill you think you got good convergence. Obviouly , you need try several times untill you got the best results! Good luck!
Jie Gao would you mind if I sent you my latest output from my IMa2 run? This time I did 400 heated chains and very long burnin (500,000). My ESS is still quite low but the trend plots maybe look better at the end of the burnin. I need some outside opinion if you don't mind. Thanks. I can email you my output.
Garima, I haven't found any software to make files for IMa2. I've spent a lot of time unhappily editing text files from fasta to .input. There are also not any utilities that work 'nicely' with IMa2 distributed with the software. I'd have to say I'm pretty disappointed with the program right now. Please, someone prove me wrong (nicely ;)
Hi. Anyone aware of developments on this, like what Garima asked: is there a software to make the input file?
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