search

todddeluca / reciprocal_smallest_distance

Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detects orthologs between genomes.
MIT License
13 stars 6 forks source link

Roundup database #5

Closed omranian closed 4 years ago

omranian commented 5 years ago

Dear Todd,

Sorry to spam you here. I couldn't get any email from you in google.

I’m interested to have the Roundup database to get access to the phylogenetic profiles; however, the provided website in your publication is not available: http://roundup.hms.harvard.edu

I would appreciate it a lot if you could please share with me the Roundup database, I’m interested in A. th. ’s phylogenetic profiles.

Thanks a lot in advance.

Kind regards, Nooshin

-- Dr. Nooshin Omranian, Systems Biology and Mathematical Modeling Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1 14476 Potsdam, Germany phone +49 (0)331 567-8548

todddeluca commented 5 years ago

Dear Nooshin,

Thanks for reaching out! I'm sorry to say that Roundup is a dead project and no longer available online.

The code for the website and computation pipeline is available at https://github.com/walllab/roundup. Theoretically, it could be run on your local computer or computational cluster, though it would probably be a bit of work to get it running.

The code for the underlying orthology algorithm is available in this repository.

Here is a list of some other orthology projects that might have what you want: https://questfororthologs.org/orthology_databases.

Please reach out if you have any questions. I'm happy to help.

Best regards, Todd

-- Todd DeLuca PhD Student, Complex Systems and Data Science University of Vermont todd.deluca@uvm.edu

On Thu, Feb 28, 2019 at 7:21 AM Nooshin Omranian notifications@github.com wrote:

Dear Todd,

Sorry to spam you here. I couldn't get any email from you in google.

I’m interested to have the Roundup database to get access to the phylogenetic profiles; however, the provided website in your publication is not available: http://roundup.hms.harvard.edu

I would appreciate it a lot if you could please share with me the Roundup database, I’m interested in A. th. ’s phylogenetic profiles.

Thanks a lot in advance.

Kind regards, Nooshin

-- Dr. Nooshin Omranian, Systems Biology and Mathematical Modeling Max-Planck-Institute of Molecular Plant Physiology Am Mühlenberg 1 14476 Potsdam, Germany phone +49 (0)331 567-8548

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/todddeluca/reciprocal_smallest_distance/issues/5, or mute the thread https://github.com/notifications/unsubscribe-auth/AANKqUOeg0vCP52uzyUdU6xSKHryHEMHks5vR8m7gaJpZM4bWsYc .