[Primeusers] Questions about duplication and loss rates
Lars Arvestad
arve at csc.kth.se
Thu Oct 13 10:45:19 CEST 2011
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 not allow unpublished paper to be included in the reference.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 handles PrIME-GEM, PrIME-GSR and some other unpublished tools as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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