Alexey Markin
@alexey-markin.bsky.social
Computational Biologist with the USDA Flu-Crew
Phylogenetics 🌳
Phylogenetic networks 🕸️
Virus evolution 🦠
https://markin-alex.github.io
Phylogenetics 🌳
Phylogenetic networks 🕸️
Virus evolution 🦠
https://markin-alex.github.io
For other stuff (eg eukaryotes) a decent strategy would be to try many random permutations of taxa and choose the best one. We implemented this strategy here
github.com/flu-crew/OLA...
3/3
github.com/flu-crew/OLA...
3/3
GitHub - flu-crew/OLA-Net: Estimation of the reticulation number via OLA vectors and leaf orderings
Estimation of the reticulation number via OLA vectors and leaf orderings - flu-crew/OLA-Net
github.com
September 24, 2025 at 6:38 PM
For other stuff (eg eukaryotes) a decent strategy would be to try many random permutations of taxa and choose the best one. We implemented this strategy here
github.com/flu-crew/OLA...
3/3
github.com/flu-crew/OLA...
3/3
If you know a good ordering of your taxa, then you can find reticulations fast (in poly-time) assuming it’s the only source of discordance among your trees or you can hide other discordance in polytomies. This is great for RNA viruses since dates of collection = good ordering
2/3
2/3
September 24, 2025 at 6:38 PM
If you know a good ordering of your taxa, then you can find reticulations fast (in poly-time) assuming it’s the only source of discordance among your trees or you can hide other discordance in polytomies. This is great for RNA viruses since dates of collection = good ordering
2/3
2/3
Not many distances out there that can be applied to large trees (other than Robinson Foulds), but cophenetic + KC now join that club. Implemented here by Sriram Vijendran: github.com/sriram98v/ne...
GitHub - sriram98v/near-linear-cophenetic-distance: Calculating generalized Cophenetic Distances in near-linear time under any Lp norm.
Calculating generalized Cophenetic Distances in near-linear time under any Lp norm. - sriram98v/near-linear-cophenetic-distance
github.com
June 21, 2025 at 9:14 PM
Not many distances out there that can be applied to large trees (other than Robinson Foulds), but cophenetic + KC now join that club. Implemented here by Sriram Vijendran: github.com/sriram98v/ne...
December 2, 2024 at 4:01 PM