I'm reposting this because I want to make a correction. In the thread below I mention using the -mset flag for testing site profile mixture models. But in fact you should use -madd flag. I'm sorry for this mistake.

Andrew Roger@andrewjroger.bsky.social · 5mo ago

So you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.

1/ Our new paper in Systematic Biology "Modeling Site-and-Branch-Heterogeneity with GFmix" led by @cgpmcc.bsky.social describes improved ways to model compositional heterogeneity across both sites and branches—an important source of error in deep phylogenomics. doi.org/10.1093/sysb...

Modeling Site-and-Branch-Heterogeneity with GFmix

Abstract. Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino a

doi.org

I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏

Hi all, we are experiencing technical difficulties with our original Zoom link. Here is an updated link: ucdavis.zoom.us/j/7241356569...

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Archaea Power Hour returns next WEDNESDAY, May 20th, at 10AM EST / 4PM CET for the final installment of our spring semester seminar series!! We have two exciting talks planned for you so check your email for the Zoom link (coming soon) or visit our website (link in bio) for more info on how to join.

🚨 Archaea alert 🚨!! We’re back this Wednesday, April 22nd, at 10 AM EST / 4 PM CET with two exciting research talks! You won’t want to miss this so check your email for the Zoom link or visit the link in our bio for more info on how to join the community 🦠

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

We have just published a short note on archaeal phylogeny: complex mixture models support a deep placement of Methanonatronarchaeia within Euryarchaea and indicate that three recently described groups (Halorutilales, Afararchaeaceae, and Ordosarchaeia) are actually the same. shorturl.at/5GMpU

So you are using IQ-TREE to estimate a tree for "deep time" phylogenetics using amino acid alignments. There is a lot of confusion about how to test model fit. Here are some suggestions.

Archaea Assemble!!! Archaea Power Hour returns next WEDNESDAY, March 18th at 11AM EST / 4PM CET. We will be having a special APH edition about science policy & reproducibility with the American Society for Microbiology and the protocol-sharing platform archaea.bio:

Beyond thrilled to share that our study has been published! This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and @texasscience.bsky.social!!! #MicroSky #ArchaeaSky 1/12

Archaea Power Hour needs you 🫵! We are looking for presenters for our upcoming spring semester seminar series now! Tell us about your amazing archaeal research by submitting an abstract here: docs.google.com/forms/u/2/d/...

Abstract Submission - Spring seminars 2026

Thank you for your interest in presenting at Archaea Power Hour! We're excited to announce that we have merged our previously separate initiatives, APH-Americas and APH-Europe, into a unified platform...

docs.google.com

A reminder to sign up for the 2026 EMBO archaeal meeting im Cambridge: meetings.embo.org/event/26-arc.... Registration is open. We are looking forward to hosting you!

Calling all archaeal enthusiasts! 🔬🔥 From molecular machines to microbial communities, Archaea never fail to surprise us! We are excited to announce the 2026 EMBO Workshop on the Molecular Biology of Archaea, 6–10 July in Cambridge, UK! Sign up here: meetings.embo.org/event/26-arc... #ArchaeaSky

#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...

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.

nature.com

Very happy to finally have this out! Thank you to my awesome PhD supervisors and all the co-authors!!

DEEMteam_Orsay@deemteam.bsky.social · last yr.

📣 We are proud of the publication of the second paper of @bbaker24.bsky.social PhD thesis. In collaboration with friends in Halifax we have studied the difficult question of the phylogeny of the DPANN archaea, composed of several phyla of highly reduced, fast-evolving epiparasites 🧵 rdcu.be/erkkU

This promises to be a cool PhD project with a very inspiring and nice PI!

Daniel Tamarit@danieltamarit.bsky.social · last yr.

New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky

It's that time again! Make sure to tune in THIS WEDNESDAY, March 12th, at 11AM EST (note the time change) / 4 PM CET to catch two exciting talks from @cjhines.bsky.social and Priyanka Chatterjee!! Check your email for the Zoom link or visit our website for more info on how to join (link in bio).

#Communiqué 🗞️ Le CNRS exprime sa solidarité avec les scientifiques exerçant aux États-Unis, où la liberté académique est aujourd'hui mise à l’épreuve. 👉 www.cnrs.fr/fr/presse/le...

Science, research & public health face unprecedented attacks in the U.S. We stand with our American colleagues & support the Stand Up for Science call. Join the global march tomorrow, incl. in Paris! 🧪✊ 📍 March 7, 13:30 – Place Jussieu 🔗 More info: standupforscience.fr #StandUpForScience

Exciting news! I'm looking for a computational biologist to join my lab at Wageningen University & Research! It's a 3-year postdoc position on Holomycota genome architecture and evolution. Spread the word! www.wur.nl/en/vacancy/p...

Postdoc Comparative genomics and genome architecture in early-diverging fungi and their protist relatives (3-year position)

wur.nl

After 3 years of work, we are thrilled to submit this preprint. In collaboration with DEEM Team, we uncovered the complex interactions between haloarchaea, nanohaloarchaea, and their respective viruses and virus satellites. See🧵 www.biorxiv.org/content/10.1... #DPANN #ArchaealViruses #Satellite

Nested parasitism in hypersaline environments: viruses and virus satellites of haloarchaea and their nanosized cellular symbionts

It is increasingly recognized that hyperparasitism, whereby a parasite exploits a host which itself is a parasite, is a common phenomenon across ecosystems and domains of life. Here, to explore hyperp...

biorxiv.org

Check out the new episode of Archaeacast! @archaealex.bsky.social and I discuss the intricacies of Thermophiles, followed with a fantastic interview by Theopi Rados with Dr. Rachel Whitaker. rss.com/podcasts/arc... Found on Apple Podcasts and Spotify! #archaea #microbiology #lifesciences #Scisky

Archaea Power Hour is back next week on WEDNESDAY, Feb. 12th at 10 AM EST / 4 PM CET! Make sure to attend and show your love for archaea this coming Valentine's week 😍🥰♥️!!! Join our mailing list to receive the Zoom link: t.co/b17JFAaZQ6.

Archaea aficionados around the world, APH is now on BlueSky! Follow us for virtual conference announcements and more 🦠

A reminder to submit abstracts for Archaea Power Hour! Researchers at all career stages are welcomed 💫 www.archaea.bio/archaea-powe...

Archaea Power Hour

Image Our MissionThe Archaea Power Hour initiative arose from a need to strengthen and g

archaea.bio

Did you miss our latest work on hypersaline and chaotropic ecosystems in the Danakil depression, where microbial communities harbour up to 99% of archaea? Go check what life looks like in these unique places: www.nature.com/articles/s41... @deemteam.bsky.social

Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines - Nature Ecology & Evolution

Metagenome analysis of microbial communities from the Danakil Depression shows that haloarchaea and Nanohaloarchaeota dominate these life-limiting salt-saturated conditions and that these archaea have...

nature.com