This week we will be meeting at the Oceanography Seminar Room on MCZ 1st floor 9-10am. Tauana Cunha will lead the discussion. Here is what she says:
Hi Phylo JC!
Next week we will be discussing orthology inference! The main paper (very short) is on benchmarking and compares several different methods. But they don’t go over details and the main differences between the methods, so I would like to ask that each of us chooses one method from the paper and look into it a bit more. A few suggestions are PANTHER: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531194/ and MetaPhOrs: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061081/, but feel free to choose another. No need to read those papers in super depth, just enough to understand what the algorithm is doing so we can compare to others.
I would like to discuss what you guys think about the main categories of methods, if you have experience with any, and if these benchmarks help us to evaluate and choose the more appropriate method for our own research.
The main paper is:
Altenhoff, A.M. et al., 2016. Standardized benchmarking in the quest for orthologs. Nature Methods, 13(5), pp.425–430.
Hi Phylo JC!
Next week we will be discussing orthology inference! The main paper (very short) is on benchmarking and compares several different methods. But they don’t go over details and the main differences between the methods, so I would like to ask that each of us chooses one method from the paper and look into it a bit more. A few suggestions are PANTHER: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531194/ and MetaPhOrs: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061081/, but feel free to choose another. No need to read those papers in super depth, just enough to understand what the algorithm is doing so we can compare to others.
I would like to discuss what you guys think about the main categories of methods, if you have experience with any, and if these benchmarks help us to evaluate and choose the more appropriate method for our own research.
The main paper is:
Altenhoff, A.M. et al., 2016. Standardized benchmarking in the quest for orthologs. Nature Methods, 13(5), pp.425–430.
altenhoff_et_al._2016_standardized_benchmarking_in_the_quest_for_orthologs.pdf |