iiinova — where your digital self keeps evolving

John Allard

@johnallard.bsky.social

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

John Allard @johnallard.bsky.social · 03/10/2026

There’s also a desktop version for Windows, macOS, and Linux, with a bundled MCP server that lets AI agents like Codex and Claude Code open, style, inspect, and export trees according to your instructions. Try it with your own tree and let me know what you think! 7/7

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John Allard @johnallard.bsky.social · 03/10/2026

Customize most visual aspects of the display, inspect whole-tree and subtree statistics, and export PNG or SVG images. Save and load sessions and settings on your computer so you can return to a configured tree later. 6/7

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John Allard @johnallard.bsky.social · 03/10/2026

Plot metadata using pie charts, colored branches, shape markers, heat maps, and more. Add organism silhouettes from phylopic.org (with attribution info), and display node labels, time uncertainties, and bootstrap values. 5/7

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John Allard @johnallard.bsky.social · 03/10/2026

It handles trees with a million tips or more, offers customizable spiral layouts, and lets you compare two trees to explore differences in clade placement. You can also re-root trees or open any subtree in a new tab or window. 4/7

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John Allard @johnallard.bsky.social · 03/10/2026

With binomial species labels (Genus species) or NCBI taxon IDs, BTV can automatically display colored ribbons corresponding to Linnaean taxonomic ranks, so you can see where major groups fall and get an idea of the topology at a glance. 3/7

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John Allard @johnallard.bsky.social · 03/10/2026

When a tree has hundreds or thousands of tips, the labels become too small to read. BTV infers genus names from tip labels and displays labeled genus bands so you can get your bearings. 2/7

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John Allard @johnallard.bsky.social · 03/10/2026

I created a demo reel showing some of the features of my web app, www.BigTreeViewer.net (BTV), for exploring and visualizing very large phylogenetic trees. Here are some of the things it can do. 🧵 1/7

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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

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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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