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John Allard

@johnallard.bsky.social

Postdoctoral researcher; Institute for Genomics and Evolutionary Medicine at Temple University.

John Allard @johnallard.bsky.social · 21/09/2026

If you look at phylogenetic trees, you might like my free full-featured browser -based tree viewer app: www.bigtreeviewer.net which can display huge trees (>100k tips, super fast), show taxonomy ribbons, make spiral trees, compare two trees, and export publication quality images. Feedback welcome!

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Reposted by John Allard

Molecular Biology and Evolution @molbioevol.bsky.social · 28/08/2026

@johnallard.bsky.social & S. Kumar present ESL-PSC Toolkit, a user-friendly software with a GUI to identify genes and sites associated with convergent traits from aligned sequences. 🔗 academic.oup.com/mbe/article/... #societyjournal #compbio

academic.oup.com

ESL-PSC Toolkit: a graphical software environment for linking shared genetic changes to convergent phenotypes

Abstract. Convergent evolution provides a useful framework for testing whether independent origins of similar traits share common genetic mechanisms. Evolu

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John Allard @johnallard.bsky.social · 27/08/2026

I’m excited to share my new paper in MBE about the graphical software toolkit I created for scanning to find convergence in amino acid sequences that underlies convergent trait evolution using our Evolutionary Sparse Learning with Paired Species Contrasts technique academic.oup.com/mbe/article/...

academic.oup.com

ESL-PSC Toolkit: a graphical software environment for linking shared genetic changes to convergent phenotypes

Abstract. Convergent evolution provides a useful framework for testing whether independent origins of similar traits share common genetic mechanisms. Evolu

143

John Allard @johnallard.bsky.social · 03/02/2026

Our review article on the genetic foundations of convergent traits was published yesterday in Nature Reviews Genetics. It covers many cases of molecular convergence and the computational methods used to find them, including new AI-based methods. You can check it out here: rdcu.be/e1T8Q

rdcu.be

The genetic foundations of convergent traits

Nature Reviews Genetics - Convergent phenotypic evolution, the independent acquisition of similar or nearly identical traits in multiple species, is widespread. Allard and Kumar explore the...

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