We can now also predict the difficulty of the multiple sequence alignment task with our new ALDiScore tool www.biorxiv.org/content/10.6...
The plot shows MSA difficulty prediction performance on completely unseen data
As animals with relatively large mouths, such as tortoises, have been extirpated from or declined on the Virgin Islands, plants with relatively large seeds have become “orphaned.” Without animals able to eat them, the seeds are not dispersed. In PNAS: https://ow.ly/KJn450Z6hqQ
Once again, thank you @jlsteenwyk.bsky.social Just keep going, please!
I have more suggestions, don't worry! I will appear 😇 Thank you so much for all your contributions to the field and for your kindness and efficiency in helping!
Large circular chromosomes -> mini circular chromosomes -> hairpin chromosomes
Huge congrats to Saelin Bjornson, a trainee I have the privilege to co-advise with Hereon Verbruggen, who has reported her analysis of the stepwise evolution of hairpin chromosomes in algae
www.cell.com/current-biol...
In a recent @annbot.bsky.social paper, Bianca Schindler and colleagues explore the distribution and conservation of a microendemic species from the Brazilian Cerrado. doi.org/10.1093/aob/...
Read more in my latest post at @botany.one!
#Botany #PlantScience #SciComm 🧪
www.botany.one/tracking-and...
Grateful to have been able to help someone by adding a new function to PhyKIT.
In v2.1.20, users can specify an occupancy threshold when creating a concatenation matrix.
jlsteenwyk.com/PhyKIT/usage...
bsky.app/profile/lati...
El levantamiento andino y la biogeografía histórica de la familia de la nuez de Brasil.
Lecythidaceae se diversificó durante el Mioceno. La mayoría de especies conservaron nichos en la selva de tierras bajas, pero varios linajes se desplazaron hacia los andes.
onlinelibrary.wiley.com/doi/10.1111/...
The most incredible phylogenetic tool! I highly recommend it to everyone in the phylogeny/genomics community. I'm sure @jlsteenwyk.bsky.social has just mastered the field! 🎉
Cássia Bitencourt
Cássia Bitencourt
Alexis Stamatakis
Proceedings of the National Academy of Sciences
Great new paper on the biogeography of the Brazil nut family #Lecythidaceae led by #UMichEEB PhD student Diana Medellín-Zabala. onlinelibrary.wiley.com/doi/10.1111/...
A multidisciplinary hunt uncovers new populations of an endemic plant, while exposing the fragile balance that keeps it from disappearing.
www.botany.one
PhyKIT v2.1.44 can now plot quartet pie charts on a phylogeny
Quartet discordance can be calculated from gene trees or parsed from ASTRAL output (-t 2)
Another feature kindly suggested by @latincassia.bsky.social!
I'm super grateful for user feedback and the opportunity to address community needs
Exciting to see @latincassia.bsky.social explore some of the new PhyKIT functions
In v.2.1.39+, figures are now highly customizable - users can specify figure width, height, font sizes, colors & more
Thank you @latincassia.bsky.social for the suggestion! Open to more great community suggestions!
Aim The assembly of tropical tree floras is complex, involving many lineage-specific histories; however, focusing on the biogeographic history of diverse clades can reveal general patterns. We inves...
PhyKIT has been undergoing a major transformation. Dozens of new functions/utilities, including plotting.
If you've used PhyKIT before or haven't taken the plunge, please do consider checking it out.
I'm really excited about expanding PhyKIT and welcome community suggestions for improvement
