[Primeusers] Questions about duplication and loss rates

[Lars Arvestad]

Oh, that is a mistake! The paper is published:
	Åkerborg Ö, Sennblad B, Arvestad L, Lagergren J (2009) Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A 106(14), 5714—5719

	Lars


Oct 12, 2011 kl. 9:41 PM skrev changdan at umich.edu:

> Thank you for your reply! On your website the recommended citation for  
> PrIME_GSR is "Åkerborg, Sennblad, Arvestad, Lagergren, Gene tree  
> analysis using a Bayesian integrated model for genes, sequences, and  
> rates, submitted". The journal I'm submitting my manuscript to does  
> not allow unpublished paper to be included in the reference. I'm  
> wondering whether your paper is in print, or are there any other ways  
> of citing PrIME_GSR? Thank you.
> 
> Best,
> 
> Dan
> 
> 
> Quoting Lars Arvestad <arve at csc.kth.se>:
> 
>> 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 handles PrIME-GEM, PrIME-GSR and some other unpublished tools as  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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> 
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