[Primeusers] Questions about duplication and loss rates

[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not allow unpublished paper to be included in the reference.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 handles PrIME-GEM, PrIME-GSR and some other unpublished tools as  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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