[Primeusers] Questions about duplication and loss rates

[Lars Arvestad]

We consider mcmc_analysis to be part of the PrIME package, since it handles PrIME-GEM, PrIME-GSR and some other unpublished tools as well, so you should not feel that you need to cite it.

	Lars



Oct 7, 2011 kl. 5:41 PM skrev changdan at umich.edu:

> Hi Lars,
> 
> Thank you for your reply. I have another question about citing the  
> "mcmc_analysis.pl". Do you have any suggestions on how I should cite  
> this perl script in my manuscript? Or is it regarded as a script  
> implemented in the PRIME_GSR program? Thank you.
> 
> Dan
> 
> 
> Quoting Lars Arvestad <arve at csc.kth.se>:
> 
>> Hi,
>> The unit is decided by how you date the species tree. So if you  
>> dated the nodes with MYA, you events per gene and MYA.
>> 
>> Lars
>> 
>> Sent from a keyboard-crippled device.
>> 
>> 5 okt 2011 kl. 22:58 skrev changdan at umich.edu:
>> 
>>> Hi all,
>>> 
>>> I have a question about the units of gene birth rate and gene death
>>> rate in the final output file. Are they duplications/losses per gene
>>> per million years? And how are these rates calculated? Sorry I could
>>> not find the info in the manual or the original paper. Thank you.
>>> 
>>> Best,
>>> 
>>> Dan
>>> 
>>> 
>>> 
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> 
> 
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