IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
Abstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih
academic.oup.com
May 6, 2026 at 5:00 PM
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...
🎉 Now out “Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free‑living euryarchaeal‑like ancestors” www.nature.com/articles/s41...
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors - Nature Microbiology
Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.
www.nature.com
June 17, 2025 at 2:25 PM
🎉 Now out “Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free‑living euryarchaeal‑like ancestors” www.nature.com/articles/s41...
Using an integrative phylogenomic approach, new research in Science reveals unprecedented phylogenomic support for sponges as the sister lineage to all other animals.
Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm
Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm
Sponging away phylogenomic incongruence
Genes with strong and consistent signals favor sponges as humans’ most distant animal relatives
scim.ag
November 19, 2025 at 8:54 PM
Using an integrative phylogenomic approach, new research in Science reveals unprecedented phylogenomic support for sponges as the sister lineage to all other animals.
Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm
Learn more in a new #SciencePerspective: https://scim.ag/4r7SLqm
January 15, 2025 at 10:20 PM
Wong et al. present IQ-TREE version 3, with new features including mixture models, gene and site concordance factors, integration with phylogenomic divergence time estimation, and a fully featured sequence simulator.
🔗 doi.org/10.1093/molbev/msag117
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msag117
#evobio #molbio #compbio
May 25, 2026 at 11:30 AM
Wong et al. present IQ-TREE version 3, with new features including mixture models, gene and site concordance factors, integration with phylogenomic divergence time estimation, and a fully featured sequence simulator.
🔗 doi.org/10.1093/molbev/msag117
#evobio #molbio #compbio
🔗 doi.org/10.1093/molbev/msag117
#evobio #molbio #compbio
New review from me and @stepheniwright.bsky.social! We argue the time is ripe for a phylogenomic approach to the study of plant sex chromosomes:
doi.org/10.32942/X2S...
doi.org/10.32942/X2S...
Plant sex chromosome evolution in the phylogenomic era
doi.org
August 14, 2026 at 1:30 PM
New review from me and @stepheniwright.bsky.social! We argue the time is ripe for a phylogenomic approach to the study of plant sex chromosomes:
doi.org/10.32942/X2S...
doi.org/10.32942/X2S...
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
November 13, 2025 at 8:34 PM
NEW pub in @science.org 🥳
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Is it sponges (panels A & B) or comb jellies (C & D) that root the animal tree of life?
For over 15 years, #phylogenomic studies have been divided.
We provide new evidence suggesting that...
🔗: www.science.org/doi/10.1126/...
Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models
ecoevorxiv.org
April 10, 2025 at 2:13 PM
Not really my announcement to make--I am but a lesser co-author--but IQ-TREE 3 has just been released!
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
(Most credit to Minh Bui and @roblanfear.bsky.social and their labs)
ecoevorxiv.org/repository/v...
If you're interested in understanding discordance in phylogenomic analyses, the @evojlinnsoc.bsky.social's special issue 'Phylogenomic Discordance: Patterns, Processes, and Solutions' is for you!
tinyurl.com/v2eces3s
I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
tinyurl.com/v2eces3s
I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
Phylogenomic Discordance: Patterns, Processes, and Solutions
Phylogenomics, the study of evolutionary relationships using genomic data, has revolutionized our understanding of the Tree of Life. As a field, phylogenomics h
academic.oup.com
September 29, 2025 at 4:00 PM
If you're interested in understanding discordance in phylogenomic analyses, the @evojlinnsoc.bsky.social's special issue 'Phylogenomic Discordance: Patterns, Processes, and Solutions' is for you!
tinyurl.com/v2eces3s
I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
tinyurl.com/v2eces3s
I'll be sharing a few articles a week until we're through the issue! (1/n)🧪
Conclusion notes that phylogenomic evidence appears inconsistent with a single spillover.
June 28, 2025 at 12:10 AM
Conclusion notes that phylogenomic evidence appears inconsistent with a single spillover.
NEW Publication!😄
Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!
🔗: tinyurl.com/yc5ja4xz
Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!
🔗: tinyurl.com/yc5ja4xz
November 25, 2024 at 5:25 PM
NEW Publication!😄
Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!
🔗: tinyurl.com/yc5ja4xz
Here, we show how #PhyKIT — a broadly applicable toolkit for #phylogenomics — can be used to construct phylogenomic data matrices (& quantify biases therein), detect anomalies in predicted orthology, calculate gene-gene coevolution, & more!
🔗: tinyurl.com/yc5ja4xz
some thoughts on new methods to root a phylogenomic tree: the smart, the symbiotic, the violent
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
New Ways to Root Phylogenomic trees: the Smart, the symbiotic, the violent
To root a phylogenomic tree is very important to study the evolutionary relationship between species. However, typically the substitution models (say GTR, LG, etc.) people use are time-reversible m…
sishuowang2022.wordpress.com
July 11, 2025 at 9:18 AM
some thoughts on new methods to root a phylogenomic tree: the smart, the symbiotic, the violent
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
From Pisani et al: CAT-GTR is one of the most flexible models in the phylogenomic arsenal.
Phylogenomic mixture models outperform homogeneous and partitioned models
academic.oup.com/mbe/advance-...
Phylogenomic mixture models outperform homogeneous and partitioned models
academic.oup.com/mbe/advance-...
Phylogenomic mixture models outperform homogeneous and partitioned models
Abstract. Significant advances have been made in resolving the tree of life, but many nodes remain debated. The last two decades saw the emergence of mixtu
academic.oup.com
April 11, 2026 at 5:55 PM
From Pisani et al: CAT-GTR is one of the most flexible models in the phylogenomic arsenal.
Phylogenomic mixture models outperform homogeneous and partitioned models
academic.oup.com/mbe/advance-...
Phylogenomic mixture models outperform homogeneous and partitioned models
academic.oup.com/mbe/advance-...
Excited to share our recent paper, which is one of the first phylogenomic analyses of copepods 🧪
TLDR: the order Harpacticoida should be split, with 2 families forming their own new order—Canuelloida
doi.org/10.1016/j.ym...
TLDR: the order Harpacticoida should be split, with 2 families forming their own new order—Canuelloida
doi.org/10.1016/j.ym...
February 28, 2025 at 4:04 AM
Excited to share our recent paper, which is one of the first phylogenomic analyses of copepods 🧪
TLDR: the order Harpacticoida should be split, with 2 families forming their own new order—Canuelloida
doi.org/10.1016/j.ym...
TLDR: the order Harpacticoida should be split, with 2 families forming their own new order—Canuelloida
doi.org/10.1016/j.ym...
Toward a phylogenomic classification of #magnoliids
New #AJB research by Andrew Helmstetter, Zacky Ezedin, Elton John de Lírio, Sylvia de Oliveira, Lars Chatrou, Roy Erkens, Isabel Larridon, @hsauquet.bsky.social et al.
doi.org/10.1002/ajb2... #botany #plantsciences #Angiosperms353 #phylogenomics
New #AJB research by Andrew Helmstetter, Zacky Ezedin, Elton John de Lírio, Sylvia de Oliveira, Lars Chatrou, Roy Erkens, Isabel Larridon, @hsauquet.bsky.social et al.
doi.org/10.1002/ajb2... #botany #plantsciences #Angiosperms353 #phylogenomics
January 15, 2025 at 3:51 PM
Toward a phylogenomic classification of #magnoliids
New #AJB research by Andrew Helmstetter, Zacky Ezedin, Elton John de Lírio, Sylvia de Oliveira, Lars Chatrou, Roy Erkens, Isabel Larridon, @hsauquet.bsky.social et al.
doi.org/10.1002/ajb2... #botany #plantsciences #Angiosperms353 #phylogenomics
New #AJB research by Andrew Helmstetter, Zacky Ezedin, Elton John de Lírio, Sylvia de Oliveira, Lars Chatrou, Roy Erkens, Isabel Larridon, @hsauquet.bsky.social et al.
doi.org/10.1002/ajb2... #botany #plantsciences #Angiosperms353 #phylogenomics
My very first post on here.
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
GhostParser: A highly scalable phylogenomic approach for the identification of ghost introgression
A growing body of empirical research shows that interspecific gene flow is a widespread biological force that shapes evolutionary histories across the Tree of Life. Computational approaches designed t...
www.biorxiv.org
August 23, 2025 at 11:52 PM
My very first post on here.
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
New #ISEPpapers #preprint by @deemteam.bsky.social: Re-evaluating the eukaryotic Tree of Life with independent phylogenomic data www.biorxiv.org/content/10.6...
#Protists #Microbes #Evolution #Eukaryotes #TreeOfLife #Phylogeny #Phylogenomics #Bioinformatics #Algae
#Protists #Microbes #Evolution #Eukaryotes #TreeOfLife #Phylogeny #Phylogenomics #Bioinformatics #Algae
April 14, 2026 at 7:37 PM
New #ISEPpapers #preprint by @deemteam.bsky.social: Re-evaluating the eukaryotic Tree of Life with independent phylogenomic data www.biorxiv.org/content/10.6...
#Protists #Microbes #Evolution #Eukaryotes #TreeOfLife #Phylogeny #Phylogenomics #Bioinformatics #Algae
#Protists #Microbes #Evolution #Eukaryotes #TreeOfLife #Phylogeny #Phylogenomics #Bioinformatics #Algae
Phylogenomic resolution of marine to freshwater dinoflagellate transitions #protists #protistsonsky
academic.oup.com
February 26, 2025 at 11:01 AM
Phylogenomic resolution of marine to freshwater dinoflagellate transitions #protists #protistsonsky
Microbiologist here. You are making it sound like either alternative is equally likely. Not so. The viral phylogenomic, geospatial and historical evidence support a zoonotic origin. No evidence supports a lab leak. It’s not a close call.
August 29, 2026 at 2:28 AM
Microbiologist here. You are making it sound like either alternative is equally likely. Not so. The viral phylogenomic, geospatial and historical evidence support a zoonotic origin. No evidence supports a lab leak. It’s not a close call.
This month's GBE Highlight by SMBE @haorancai.bsky.social focuses on the recent paper by Bastian, Enard & Lartillot on the nearly neutral theory.
"Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals"
🔗 doi.org/10.1093/gbe/evag074
#genome #evolution
"Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals"
🔗 doi.org/10.1093/gbe/evag074
#genome #evolution
April 24, 2026 at 11:00 AM
This month's GBE Highlight by SMBE @haorancai.bsky.social focuses on the recent paper by Bastian, Enard & Lartillot on the nearly neutral theory.
"Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals"
🔗 doi.org/10.1093/gbe/evag074
#genome #evolution
"Bridging Micro- and Macroevolution: Phylogenomic Evidence for the Nearly Neutral Theory in Mammals"
🔗 doi.org/10.1093/gbe/evag074
#genome #evolution
Reticulated adaptive radiation and phylogenomic diversityloss in the Hawaiian honeycreepers #ornithology www.pnas.org/doi/epdf/10....
August 5, 2026 at 3:59 PM
Reticulated adaptive radiation and phylogenomic diversityloss in the Hawaiian honeycreepers #ornithology www.pnas.org/doi/epdf/10....
And one more x.com/phylogenomic...
x.com
September 9, 2025 at 3:00 AM
And one more x.com/phylogenomic...
ASTER: A Package for Large-scale Phylogenomic Reconstructions. #Phylogenomics #SpeciesTreeInference @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/advance-...
academic.oup.com/mbe/advance-...
July 27, 2025 at 6:05 PM
ASTER: A Package for Large-scale Phylogenomic Reconstructions. #Phylogenomics #SpeciesTreeInference @molbioevol.bsky.social 🧬 🖥️
academic.oup.com/mbe/advance-...
academic.oup.com/mbe/advance-...
Happy to have been part of this new article on planthopper (Fulgoromorpha) systematics! A great collaboration between Jagiellonian and Lund Universities!
doi.org/10.1111/syen...
doi.org/10.1111/syen...
Phylogenomic insights into the relationship and the evolutionary history of planthoppers (Insecta: Hemiptera: Fulgoromorpha)
Using genomic data from 285 species across 19 planthopper families, we conducted the first phylogenomic study targeting global planthoppers and inferred their phylogeny with the highest resolution s.....
doi.org
January 3, 2025 at 7:46 AM
Happy to have been part of this new article on planthopper (Fulgoromorpha) systematics! A great collaboration between Jagiellonian and Lund Universities!
doi.org/10.1111/syen...
doi.org/10.1111/syen...
#NewResearch
🚨Out Now
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team
#MicroSky #Archaea 🦠
www.nature.com/articles/s41...
🚨Out Now
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team
#MicroSky #Archaea 🦠
www.nature.com/articles/s41...
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors - Nature Microbiology
Phylogenetic reconstructions with conserved protein markers from the 11 known DPANN phyla reveal their monophyletic placement within the Euryarchaeota.
www.nature.com
June 18, 2025 at 1:53 PM
#NewResearch
🚨Out Now
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team
#MicroSky #Archaea 🦠
www.nature.com/articles/s41...
🚨Out Now
Phylogenomic analyses indicate the archaeal superphylum DPANN originated from free-living euryarchaeal-like ancestors, by @bbaker24.bsky.social @deemteam.bsky.social and team
#MicroSky #Archaea 🦠
www.nature.com/articles/s41...