If you're into old phylogenetics methods and want to contribute ideas, fork it. if you find a bug in C code you'd rather not touch, file an issue and I'll probably fix it. If you use it for something weird, let me know.
chriscreevey.github.io/clann/
The per-source-tree score matrix in 'usertrees' is probably the most practical addition. Tells you exactly which source trees drives decisions between multiple topologies and which ones are just along for the ride. Makes it easy to spot dodgy source trees pulling at your supertree.
The landscape analysis feature records every tree visited during heuristic search, and can cluster them by RF distance, see the shape of your treespace. not sure if anyone's doing supertree inference of this kind anymore but if you are, this might be useful.
I have wanted to implement the maximum likelihood heuristic search for forever, and it's quick enough to carry out heuristic searches. This is based on a nifty 64-bit integer hash trick for Robinson Foulds comparisons that works super fast.
I've spent far too much time resurrecting Clann, the 23(!) year old supertree tool nobody asked for but apparently I couldn't let die 😅
V5.1: Now with ML & RF criteria, ML topology tests, OpenMP parallelisation, source-tree weighting, landscape clustering & a python API github.com/ChrisCreevey...
Last chance to apply for our funded PhD opportunity. w. Prof. Fredric Coulon @ Cranfield University. This will investigate expansion of ML models for AMR phenotype detection to agriculture settings to create a sensor-ready hit list.
Detail here:
www.findaphd.com/phds/project...
Excited to share our lab’s latest paper in Microbiome! 🧬 We’ve developed "ProFiT-SPEci-FISH", a new pipeline to solve a classic problem: linking plasmids to their specific bacterial hosts in complex samples like the human gut. (1/7)
link.springer.com/article/10.1...
Fully funded #PhD project available for Oct 26 start FoodBioSystems DTP w. Prof. Fredric Coulon @ Crandfield University. This will investigate expansion of ML models for AMR phenotype detection to agriculture settings to create a sensor-ready hit list. More info: www.findaphd.com/phds/project...
Photo of presentation in action with a a complex graph on screen
Photo of presentation in action with a large phylogenetic tree on the screen
Groups photo of the meeting participants
Its been an incredible three days of outstanding science at the Holoruminant.eu annual meeting here in QUB. Its such a privilege to host this amazing team. As we enter the final year of the project, there are so many exciting papers and tools to come. #EUH2020 #ruminant #microbiology
James has done a great job of putting our latest preprint in context, led by @lucydillon.bsky.social. A combined ML and pangenome approach of over 16K genomes reveals the possibility of evolutionary dead ends in MDR organisms that could be exploited therapeutically. @qubelfastofficial.bsky.social
New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...
Presentation of the new degree programmes
Wonderful to see the launch of the School of Biological Sciences! 🎓 @qubelfastofficial.bsky.social newest undergraduate degree programmes!
BSc Agricultural Sciences and BSc/MSci Veterinary Biosciences - exciting opportunities for the next generation of scientists
#HE #Degrees
Science is the ultimate team sport! Next week @qubelfastofficial.bsky.social hosts researchers from 15 countries for the EU H2020 HoloRuminant project. International collaboration, different perspectives, shared data, common goals! 🌍🐄 Looking forward to it!
#HoloRuminant #MicrobialEcology #EUH2020
Our newest title, Microbiology Outlooks is now open to submissions! If you have a review, perspective, or commentary to contribute, submit to this forward-looking journal covering all areas of microbiology research: microb.io/Mout. #NewJournal #Mout
I missed this when it came out last September - excellent essay!
Not-so-mutually beneficial coral symbiosis: Current Biology www.cell.com/current-biol...
Is there only one "path" that evolution tends to take when a new trait arises? Or can the trait arise in more than one way? In other words, walking back from a particular evolutionary "destination", do we always take the same path? The answer might be "no", at least some of the time. In fact... 1/n
New preprint from the group: @lucydillon.bsky.social analysis of 16,000+ genomes finds Bacteria cannot combine certain resistance genes as they are mutually exclusive, forcing them down incompatible evolutionary paths.
biorxiv.org/content/10.1101/2025.08.20.671315v1
@jomcinerney.bsky.social
Available now:
Fully funded 4-year PhD studentship (with BBSRC NILAB)
Integrating AI and Taxonomy-Free Classification for Enhanced Microbiome Analysis of One Health Environments.
Merging AI & microbiomics to drive impactful advancements in One Health.
Apply here:
www.qub.ac.uk/courses/post...
Final day! You have until 23:59 GMT+0 March 10 to apply yo the LinneSys scheme.
We (@systassn.bsky.social and @linneansociety.bsky.social) provide up to 1500GBP for taxonomy and/or systematics projects.
You just need to be a member to apply.
Apply TODAY: systass.org/linnesys/
On the eve of international women’s day, it’s worth being reminded why it’s so important.
It's #DarwinDay! Here is Charles Darwin as part of the series "Men of the Day" (1871) from Vanity Fair (UK), a weekly magazine. Unsigned chromolithograph by James Jacques Tissot that is accompanied by an article by Thomas Gibson Bowles.
Read here: bit.ly/40S5cdP
#OnThisDay in 1941 the first patient, Albert Alexander, was treated with Penicillin. This event marked the success of antibiotics and their application in medicine. His story serves as a testament to inspire researchers to develop new life-saving antibiotics in an effort against AMR #KnockingOutAMR
Love this :D
Congratulations DR @cmkobel.bsky.social on the successful defense of your thesis 🙌🏼 Massive thanks to @hairyllama.bsky.social and @manuelkleiner.bsky.social for the time and your style which made the day all the more entertaining.
First up a bioinformatics project with Dr Wayne Aubrey Small but mighty. Small Genes, Big Impact: Exploring sORFs in Host-Parasite Interactions www.findaphd.com/phds/project...
3 funded PhD opportunities to work with me and my new lab. 2 led by me and the other I will co-supervise with parasitologist Prof. Geoff Gobert, QUB.
#PhD #bioinformatics #Genomics #AI #biodiversity
See next post to find out about these projects! 👇
#PhD 1: Effects of Mercury in Amazonian Amphibians 🐸 as part of BBSRC funded NorthWestBio DTP. Based at @qubelfastofficial.bsky.social
Project: tinyurl.com/frogHg
Apply: tinyurl.com/NWBapply
Deadline: 06/01/2025
He’s making a list…
Congrats Lucy! It’s well deserved! It’s been a pleasure working with you.
