[Inparanoid] orthologous gene assign

[Erik Sonnhammer]

Hi Jun,

If the 4 species are "evolutionarily equidistant" from each other, then 
you can try to use MultiParanoid, http://multiparanoid.sbc.su.se/

Also Hieranoid http://hieranoid.sbc.su.se/ may work, but we acknowledge 
that Hieranoid has some issues with accuracy at the moment.

Bests
Erik Sonnhammer

On 04/26/2014 08:10 PM, Jun Wang wrote:
>
> Hi,
>
> I am now dealing with the comparative genomic project, I want to do 
> orthologous analysis, so I use this inparanoid4.1 software, and it is 
> good. While my problem is: I have more than two species, for example, 
> I have four species (A, B, C, D), how can do it with inparanoid 
> software in order to have the orthologous gene among the four species. 
> Should I do like this (AB, AC, AD, BC, BD, CD)? And then extract the 
> orthologous gene name manually? Thank you very much, I really 
> appreciate it!
>
> Bests,
>
> Jun Wang
>
> University of Nebraska at Omaha
>
>
>
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