Ziheng Yang Lab
@zihengyang.bsky.social
Ziheng Yang's Lab at UCL (CLOE) | Computational Molecular Evolution
Website: http://abacus.gene.ucl.ac.uk/
BPP GitHub: https://github.com/bpp/
PAML GitHub: https://github.com/abacus-gene/paml
PAML discussion group: https://groups.google.com/g/pamlsoftware
Website: http://abacus.gene.ucl.ac.uk/
BPP GitHub: https://github.com/bpp/
PAML GitHub: https://github.com/abacus-gene/paml
PAML discussion group: https://groups.google.com/g/pamlsoftware
We have had a great time at the Workshop on Computational Genomics at Beijing Normal University! Thank you to all organisers, course assistants, and the fantastic and hard-working participants for making this event possible! 下次见, 谢谢 🌹(1/2)
November 11, 2025 at 6:05 AM
We have had a great time at the Workshop on Computational Genomics at Beijing Normal University! Thank you to all organisers, course assistants, and the fantastic and hard-working participants for making this event possible! 下次见, 谢谢 🌹(1/2)
Reposted by Ziheng Yang Lab
First up we have Xiyun Jiao and @zihengyang.bsky.social showing the importance of moving beyond model fit testing and embracing sensitivity testing in phylogenetics.
In other words, question your data assumptions and test for model robustness not just adequacy.
(2/n)
doi.org/10.1093/evol...
In other words, question your data assumptions and test for model robustness not just adequacy.
(2/n)
doi.org/10.1093/evol...
On measures of influence and discordance in phylogenomic analyses
Abstract. As models are approximate descriptions of real biological processes, and data are collected often with errors and contamination, sensitivity or r
doi.org
September 29, 2025 at 4:00 PM
First up we have Xiyun Jiao and @zihengyang.bsky.social showing the importance of moving beyond model fit testing and embracing sensitivity testing in phylogenetics.
In other words, question your data assumptions and test for model robustness not just adequacy.
(2/n)
doi.org/10.1093/evol...
In other words, question your data assumptions and test for model robustness not just adequacy.
(2/n)
doi.org/10.1093/evol...
Reposted by Ziheng Yang Lab
Ji, Kapli, Flouri & @zihengyang.bsky.social assess the impact of genotyping errors in phylogenomic data on Bayesian inference of species trees, suggesting that it is better to sequence a few samples at high depths over many samples at low depths.
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model
Abstract. The multispecies coalescent (MSC) model accounts for genealogical fluctuations across the genome and provides a framework for analyzing genomic d
doi.org
August 19, 2025 at 7:35 PM
Ji, Kapli, Flouri & @zihengyang.bsky.social assess the impact of genotyping errors in phylogenomic data on Bayesian inference of species trees, suggesting that it is better to sequence a few samples at high depths over many samples at low depths.
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf184
#evobio #molbio
Reposted by Ziheng Yang Lab
In the first Plenary speech of #SMBE2025, Ziheng Yang (@zihengyang.bsky.social) taught us quite a few improbable things on gene flow.
We wish you a delicious breakfast for tomorrow, while mulling over these lessons... 😉
We wish you a delicious breakfast for tomorrow, while mulling over these lessons... 😉
July 20, 2025 at 4:18 PM
In the first Plenary speech of #SMBE2025, Ziheng Yang (@zihengyang.bsky.social) taught us quite a few improbable things on gene flow.
We wish you a delicious breakfast for tomorrow, while mulling over these lessons... 😉
We wish you a delicious breakfast for tomorrow, while mulling over these lessons... 😉
Reposted by Ziheng Yang Lab
Using simulations and empirical data, Thawornwattana, Flouri, @wtf-r-species.bsky.social & @zihengyang.bsky.social et al. evaluate the performance of the MSC-M model for inferring gene flow.
🔗 doi.org/10.1093/molbev/msaf121
#evobio #molbio #geneflow
🔗 doi.org/10.1093/molbev/msaf121
#evobio #molbio #geneflow
Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified
Abstract. Thanks to genomic data, interspecific gene flow is increasingly recognized as a major evolutionary force that shapes biodiversity. Two models hav
doi.org
July 1, 2025 at 7:12 AM
Using simulations and empirical data, Thawornwattana, Flouri, @wtf-r-species.bsky.social & @zihengyang.bsky.social et al. evaluate the performance of the MSC-M model for inferring gene flow.
🔗 doi.org/10.1093/molbev/msaf121
#evobio #molbio #geneflow
🔗 doi.org/10.1093/molbev/msaf121
#evobio #molbio #geneflow
Reposted by Ziheng Yang Lab
The first Keynote speech of #SMBE2025 will be given by SMBE's President Ziheng Yang (@zihengyang.bsky.social).
"Six impossible things to believe before breakfast, about gene flow"
20.07.2025 | 18h00
"Six impossible things to believe before breakfast, about gene flow"
20.07.2025 | 18h00
June 23, 2025 at 9:02 AM
The first Keynote speech of #SMBE2025 will be given by SMBE's President Ziheng Yang (@zihengyang.bsky.social).
"Six impossible things to believe before breakfast, about gene flow"
20.07.2025 | 18h00
"Six impossible things to believe before breakfast, about gene flow"
20.07.2025 | 18h00
What a busy (but sunny) May in Crete!🔆 Ziheng & @sabifo4.bsky.social enjoyed teaching and meeting the participants at the Computational Molecular Evolution course! Ziheng then joined the satellite workshop on Biodiversity Genomics 🌍🧬 Thanks to everyone who made these fantastic meetings possible!!
June 6, 2025 at 2:15 PM
What a busy (but sunny) May in Crete!🔆 Ziheng & @sabifo4.bsky.social enjoyed teaching and meeting the participants at the Computational Molecular Evolution course! Ziheng then joined the satellite workshop on Biodiversity Genomics 🌍🧬 Thanks to everyone who made these fantastic meetings possible!!
Congratulations Dr Jiayi Ji!! 🥳Thanks to examiners @hernanaburbano.bsky.social and Simon Martin, now time to enjoy the long weekend! 🎉
May 2, 2025 at 8:06 PM
Congratulations Dr Jiayi Ji!! 🥳Thanks to examiners @hernanaburbano.bsky.social and Simon Martin, now time to enjoy the long weekend! 🎉
Reposted by Ziheng Yang Lab
And that's a wrap on the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop!
Thank you to all the attendees, instructors (@anaserrasilva.bsky.social, @sabifo4.bsky.social, Tomas Flouri and Yuttapong Thawornwattana) and to our wonderful TA @lauramulvey.bsky.social!
Thank you to all the attendees, instructors (@anaserrasilva.bsky.social, @sabifo4.bsky.social, Tomas Flouri and Yuttapong Thawornwattana) and to our wonderful TA @lauramulvey.bsky.social!
April 30, 2025 at 6:22 PM
And that's a wrap on the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop!
Thank you to all the attendees, instructors (@anaserrasilva.bsky.social, @sabifo4.bsky.social, Tomas Flouri and Yuttapong Thawornwattana) and to our wonderful TA @lauramulvey.bsky.social!
Thank you to all the attendees, instructors (@anaserrasilva.bsky.social, @sabifo4.bsky.social, Tomas Flouri and Yuttapong Thawornwattana) and to our wonderful TA @lauramulvey.bsky.social!
The 2nd day of the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop was focused on the Multispecies Coalescent Theory and the usage of BPP, led by our lab members Tomas Flouri and Yuttapong Thawornwattana! 💻🧬
Day 2 of our (@systassn.bsky.social and SRUK/CERU) joint Bayesian Phylogenetics Workshop is underway!
We started with an introduction to the Multispecies Coalescent by Yuttapong Thawornwattana.
We started with an introduction to the Multispecies Coalescent by Yuttapong Thawornwattana.
May 1, 2025 at 9:05 AM
The 2nd day of the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop was focused on the Multispecies Coalescent Theory and the usage of BPP, led by our lab members Tomas Flouri and Yuttapong Thawornwattana! 💻🧬
The SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop started yesterday! During the 1st day, our lab members Tomas Flouri, @anaserrasilva.bsky.social, and @sabifo4.bsky.social had fun sharing their knowledge on Bayesian statistics, phylogeny inference & timetree inference with the participants💻🧬
The first joint @systassn.bsky.social and SRUK/CERU Bayesian Phylogenetics Workshop is underway!
April 30, 2025 at 11:15 AM
The SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop started yesterday! During the 1st day, our lab members Tomas Flouri, @anaserrasilva.bsky.social, and @sabifo4.bsky.social had fun sharing their knowledge on Bayesian statistics, phylogeny inference & timetree inference with the participants💻🧬
Our Workshop on Genomics at Sun Yat-sen University Institute of Advanced Studies Hong Kong has come to an end! We are grateful to all organisers and very pleased to have meet such fantastic and hard-working participants! 下次见, 谢谢 🌹(1/2)
March 6, 2025 at 9:39 AM
Our Workshop on Genomics at Sun Yat-sen University Institute of Advanced Studies Hong Kong has come to an end! We are grateful to all organisers and very pleased to have meet such fantastic and hard-working participants! 下次见, 谢谢 🌹(1/2)
Our lab members @sabifo4.bsky.social, @anaserrasilva.bsky.social, Tomas Flouri, and Yuttapong Thawornwattana are teaching a two-day workshop on Bayesian Phylogenetics Workshop 💻🧬 Pre-register your interest to join this event before March 14th, do not miss the deadline! More details below 🔽
We are organising an in-person Bayesian Phylogenetics Workshop, in partnership with SRUK/CERU.
When: April 29-30, 2025
Where: University College London
There are limited places, so please pre-register by March 14th!!!
Find more details here: systass.org/workshop-bay...
When: April 29-30, 2025
Where: University College London
There are limited places, so please pre-register by March 14th!!!
Find more details here: systass.org/workshop-bay...
February 19, 2025 at 5:49 PM
Our lab members @sabifo4.bsky.social, @anaserrasilva.bsky.social, Tomas Flouri, and Yuttapong Thawornwattana are teaching a two-day workshop on Bayesian Phylogenetics Workshop 💻🧬 Pre-register your interest to join this event before March 14th, do not miss the deadline! More details below 🔽
Thinking of starting a PhD on Bayesian phylogenetics next October 2025 in London? 🎓
You may want to check the TREES project led by the dos Reis Lab on integrating morphology and genomes for timetree inference! 🦴🧬💻Project supervisors: @mariodosreis.bsky.social & Ziheng Yang. More info in link 🔽
You may want to check the TREES project led by the dos Reis Lab on integrating morphology and genomes for timetree inference! 🦴🧬💻Project supervisors: @mariodosreis.bsky.social & Ziheng Yang. More info in link 🔽
We have a project on Bayesian phylogenetics: www.trees-dla.ac.uk/projects/int... with @zihengyang.bsky.social
Integrating morphology and genomes to infer evolutionary timescales | UCL Trees
Large biological datasets are accumulating at a fast pace, such as genome sequences from the EarthBiogenome project or 3D scan data from museum specimens. These datasets can be integrated to resolve e...
www.trees-dla.ac.uk
December 9, 2024 at 12:09 PM
Thinking of starting a PhD on Bayesian phylogenetics next October 2025 in London? 🎓
You may want to check the TREES project led by the dos Reis Lab on integrating morphology and genomes for timetree inference! 🦴🧬💻Project supervisors: @mariodosreis.bsky.social & Ziheng Yang. More info in link 🔽
You may want to check the TREES project led by the dos Reis Lab on integrating morphology and genomes for timetree inference! 🦴🧬💻Project supervisors: @mariodosreis.bsky.social & Ziheng Yang. More info in link 🔽
Reposted by Ziheng Yang Lab
Wrapping up an incredible 5-day course on #Phylogenomics with a fascinating lecture on Molecular-Clock dating of species divergence by @mariodosreis.bsky.social, followed by a hands-on session with @sabifo4.bsky.social 🧬🕰️
Huge thanks to all participants for an inspiring week!@zihengyang.bsky.social
Huge thanks to all participants for an inspiring week!@zihengyang.bsky.social
December 6, 2024 at 11:12 AM
Wrapping up an incredible 5-day course on #Phylogenomics with a fascinating lecture on Molecular-Clock dating of species divergence by @mariodosreis.bsky.social, followed by a hands-on session with @sabifo4.bsky.social 🧬🕰️
Huge thanks to all participants for an inspiring week!@zihengyang.bsky.social
Huge thanks to all participants for an inspiring week!@zihengyang.bsky.social
Reposted by Ziheng Yang Lab
Here’s the amazing Phylogenomics Group 2024 📸
Thank you to our incredible instructors for sharing their knowledge and making complex topics approachable and engaging! 🙌
And a big shoutout to all participants—Thanks for joining us this week🎉 @sabifo4.bsky.social @zihengyang.bsky.social
Thank you to our incredible instructors for sharing their knowledge and making complex topics approachable and engaging! 🙌
And a big shoutout to all participants—Thanks for joining us this week🎉 @sabifo4.bsky.social @zihengyang.bsky.social
December 5, 2024 at 11:53 AM
Here’s the amazing Phylogenomics Group 2024 📸
Thank you to our incredible instructors for sharing their knowledge and making complex topics approachable and engaging! 🙌
And a big shoutout to all participants—Thanks for joining us this week🎉 @sabifo4.bsky.social @zihengyang.bsky.social
Thank you to our incredible instructors for sharing their knowledge and making complex topics approachable and engaging! 🙌
And a big shoutout to all participants—Thanks for joining us this week🎉 @sabifo4.bsky.social @zihengyang.bsky.social
Reposted by Ziheng Yang Lab
🚨 Exciting Day 3 Ahead! 🚨
Today, we’re honored to have one of the giants of Phylogenomics 🧬✨, @zihengyang.bsky.social, kicking off the day with two lectures on the Multispecies Coalescent Model.
Day3 will continue with an hands-on session led by Paschalia Kapli and Tomas Flouri🚀
Today, we’re honored to have one of the giants of Phylogenomics 🧬✨, @zihengyang.bsky.social, kicking off the day with two lectures on the Multispecies Coalescent Model.
Day3 will continue with an hands-on session led by Paschalia Kapli and Tomas Flouri🚀
December 4, 2024 at 12:50 PM
🚨 Exciting Day 3 Ahead! 🚨
Today, we’re honored to have one of the giants of Phylogenomics 🧬✨, @zihengyang.bsky.social, kicking off the day with two lectures on the Multispecies Coalescent Model.
Day3 will continue with an hands-on session led by Paschalia Kapli and Tomas Flouri🚀
Today, we’re honored to have one of the giants of Phylogenomics 🧬✨, @zihengyang.bsky.social, kicking off the day with two lectures on the Multispecies Coalescent Model.
Day3 will continue with an hands-on session led by Paschalia Kapli and Tomas Flouri🚀
Reposted by Ziheng Yang Lab
✨ Day 2 highlight! ✨ Tomas Flouri and @sabifo4.bsky.social delivered masterful lectures and an exceptional hands-on session on Bayesian inference in Phylogenomics. 🎓💡 Their expertise truly shone through!
Excited for the insights Day 3 will bring—stay tuned! 🚀
Excited for the insights Day 3 will bring—stay tuned! 🚀
December 4, 2024 at 9:22 AM
✨ Day 2 highlight! ✨ Tomas Flouri and @sabifo4.bsky.social delivered masterful lectures and an exceptional hands-on session on Bayesian inference in Phylogenomics. 🎓💡 Their expertise truly shone through!
Excited for the insights Day 3 will bring—stay tuned! 🚀
Excited for the insights Day 3 will bring—stay tuned! 🚀
The Physalia Phylogenomics course has started today! Tomas and Paschalia are leading today's session -- now, they are going through the practical session to apply all the concepts they have taught this morning! 💻
Amazing course with an amazing team of instructors.
The Phylogenomics course has just started :) @sabifo4.bsky.social @zihengyang.bsky.social
The Phylogenomics course has just started :) @sabifo4.bsky.social @zihengyang.bsky.social
December 2, 2024 at 3:13 PM
The Physalia Phylogenomics course has started today! Tomas and Paschalia are leading today's session -- now, they are going through the practical session to apply all the concepts they have taught this morning! 💻
If you have ever wondered whether the PAML documentation could be more interactive... We have good news for you! The PAML GitHub repository has been updated and a fresh PAML Wiki is now available for you to navigate the PAML documentation! 📄💻 (1/n)
github.com/abacus-gene/...
github.com/abacus-gene/...
HOME
PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, pr...
github.com
November 29, 2024 at 2:26 PM
If you have ever wondered whether the PAML documentation could be more interactive... We have good news for you! The PAML GitHub repository has been updated and a fresh PAML Wiki is now available for you to navigate the PAML documentation! 📄💻 (1/n)
github.com/abacus-gene/...
github.com/abacus-gene/...
Hello BlueSky!
The Ziheng Yang Lab will be using this social account to post news about the software we develop, upcoming workshops, and general news in evolutionary biology and computational methods 💻🧬🦴
Keep an eye on this site, we will be posting some news soon!
The Ziheng Yang Lab will be using this social account to post news about the software we develop, upcoming workshops, and general news in evolutionary biology and computational methods 💻🧬🦴
Keep an eye on this site, we will be posting some news soon!
November 28, 2024 at 12:13 PM
Hello BlueSky!
The Ziheng Yang Lab will be using this social account to post news about the software we develop, upcoming workshops, and general news in evolutionary biology and computational methods 💻🧬🦴
Keep an eye on this site, we will be posting some news soon!
The Ziheng Yang Lab will be using this social account to post news about the software we develop, upcoming workshops, and general news in evolutionary biology and computational methods 💻🧬🦴
Keep an eye on this site, we will be posting some news soon!