@David__Emms

Developer of OrthoFinder and https://xitter.cf/t.co/pWdIdp8atF, interested in phylogenomics and all things trees. Former postdoc in the @Steve__Kelly lab.

github.com/davidemms/OrthoFinder
Joined September 2017
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SHOOT, the phylogenetic sequence search engine, has been published! SHOOT is like BLAST, but instead of a list of similar sequences you get a maximum likelihood phylogenetic tree for your query gene sequence. Try it👉 shoot.bio Article👉 bit.ly/3qLGb2N
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David Emms retweeted
DrBelcher@dr_belcher16 Jul 2025
OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/Ortho… biorxiv.org/content/10.1101/…

GitHub - OrthoFinder/OrthoFinder: Phylogenetic orthology inference for comparative genomics

Phylogenetic orthology inference for comparative genomics - OrthoFinder/OrthoFinder

github.com
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It has been a while… but an updated, faster & more accurate version of OrthoFinder is now out! Scales to thousands of species on conventional compute resources with higher accuracy than ever before and the same data rich fully phylogenetic outputs 👉biorxiv.org/content/10.1101/…

OrthoFinder: scalable phylogenetic orthology inference for comparative genomics

Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder’s high accuracy comparative genomic framework to provide substantially enhanced scalability and accuracy. Specif...

biorxiv.org
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We have a new version of OrthoFinder: biorxiv.org/content/10.1101/… Faster scaling to larger species sets, phylogenetically resolved orthogroups, reduced RAM usage. Thanks to @dr_belcher, Yi Liu & Jonathan Holmes who have joined the team, and as ever OrthoFinder's PI @Steve__Kelly!
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And with the new OrthoFinder team we have a new website to bookmark for all the latest updates: github.com/OrthoFinder/Ortho…

GitHub - OrthoFinder/OrthoFinder: Phylogenetic orthology inference for comparative genomics

Phylogenetic orthology inference for comparative genomics - OrthoFinder/OrthoFinder

github.com
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I've moved to new pastures, working on AI models for genomics at the excellent @instadeepai, but will carry on supporting the OrthoFinder team in the background. They're going to be working on some great, new functionality so keep an eye open for that: github.com/OrthoFinder/Ortho…

GitHub - OrthoFinder/OrthoFinder: Phylogenetic orthology inference for comparative genomics

Phylogenetic orthology inference for comparative genomics - OrthoFinder/OrthoFinder

github.com
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We are looking for a postdoc in comparative genomics/bioinformatics! They will be working in a collaborative environment on an exciting project about synteny, orthology, evolution, gene loss and 🍅. Details: tinyurl.com/4fenkydr Please share! @DessimozLab @SebastianSoyk – at Lausanne, Switzerland
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#PhD or #Postdoc using #genomics🧬 to study non-model eukaryotes 🐸🐌🌿 in #Europe? Join the #European Reference #Genome Atlas @erga_biodiv to participate in webinars, committee actions, #training: collaborative #biodiversity data production & analysis erga-biodiversity.eu/ergacal…
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Please RT Last few days left to apply! 4 positions to join us at Oxford, driving the next phase of development to OrthoFinder 🧬 We have so many cool ideas and fun things to try. Lets enhance the communities comparative genome capability together! 👉shorturl.at/gtHKT
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SHOOT, from @David__Emms & @Steve__Kelly, searches for a sequence in a database of phylogenetic trees, identifies the homology group, and places that sequence in the phylogeny. It finds closest related sequence better than BLAST, with similar speed genomebiology.biomedcentral.…
Schematic of SHOOT. It generates a database of phylogenies. A sequence can then be queried against the multiple sequence alignments, and placed on a tree

ALT Schematic of SHOOT. It generates a database of phylogenies. A sequence can then be queried against the multiple sequence alignments, and placed on a tree

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You give SHOOT.bio a query sequence and it builds a gene tree and identifies the orthologs of your gene in other species Try it👉 shoot.bio Article👉 bit.ly/3qLGb2N
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SHOOT.bio is powered by OrthoFinder, DIAMOND, IQ-TREE, MAFFT, EPA-ng & phylotree.js with some other clever technologies under the hood to accelerate your search and gene tree inference. Try it👉 shoot.bio Article👉 bit.ly/3qLGb2N
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We have TWO fully funded PhD studentships available in our group to study 3D growth in plants. Both studentships are available from October 2022. Please get in touch if you’re interested. Please do retweet and/or spread the word 😃 🧬 🌱
Propidium iodide stained buds of Physcomitrium patens WT and also a variety of developmental mutants that fail to establish and/or maintain 3D growth.

ALT Propidium iodide stained buds of Physcomitrium patens WT and also a variety of developmental mutants that fail to establish and/or maintain 3D growth.

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The preprint describing our comparative genomics #Rstats package is on bioRxiv (link below). GENESPACE uses synteny to explore variation among multiple genomes. For example, here are the syntenic regions to the human X and chicken Z sex chromosomes across 17 vertebrates
Structural evolution of mammalian X and avian Z sex chromosomes. The reptilian, avian, and mammalian sex chromosomes syntenic network across 17 representative vertebrate genomes (two reptile, five eutherian mammal, three marsupial, two monotremes, and five avian). The plot was generated by the GENESPACE function plot_riparian. Genomes are ordered vertically to maximize synteny between sequential pairwise genomes. Chromosomes are ordered horizontally to maximize synteny with the human chromosomes [X, Y, 1-22]. Regions containing syntenic orthogroup members to the mammalian X (gold) or avian Z (blue) chromosomes are highlighted. Take-homes: (1) sand lizard Z chromsomes is related to mammalian X, but not avian Z, (2) the budgie Z chromosome has a neo-autosomal fusion absent in all other birds, (3) monotreme X chromomes (which are weird) are non-syntenic with mammalian X, but partially related to the avian Z.

ALT Structural evolution of mammalian X and avian Z sex chromosomes. The reptilian, avian, and mammalian sex chromosomes syntenic network across 17 representative vertebrate genomes (two reptile, five eutherian mammal, three marsupial, two monotremes, and five avian). The plot was generated by the GENESPACE function plot_riparian. Genomes are ordered vertically to maximize synteny between sequential pairwise genomes. Chromosomes are ordered horizontally to maximize synteny with the human chromosomes [X, Y, 1-22]. Regions containing syntenic orthogroup members to the mammalian X (gold) or avian Z (blue) chromosomes are highlighted. Take-homes: (1) sand lizard Z chromsomes is related to mammalian X, but not avian Z, (2) the budgie Z chromosome has a neo-autosomal fusion absent in all other birds, (3) monotreme X chromomes (which are weird) are non-syntenic with mammalian X, but partially related to the avian Z.

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Plant Science Research Weekly plantae.org/plant-science-re… X-species sRNAs, SynBio -> N fixation, gene evolution & organelles, land plant evolution, archaeon at the prok–euk interface, SMXL & phloem, reclassifying filamentous pathogens, drought stress & mycobiomes, and more!
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Our GENESPACE comparative genomics R package is on github! GENESPACE conducts synteny-constrained comparisons of gene copy number and presence absence variation among genomes of any ploidy, and makes graphics like this (synteny among grasses, colored by rice chromosomes):
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The preprint for the SHOOT.bio gene search website with @Steve__Kelly has been updated: bit.ly/3BDiyfD SHOOT lets you search a protein sequence & get back a maximum likelihood gene tree for your sequence. It's a robust & easy way to get accurate orthologs.
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The source code for the command line version is on GitHub: github.com/davidemms/SHOOT There's also code on GitHub for a SHOOT webserver. If you're interested in adapting it to enable phylogenetic gene search for a genome resource website, let me know!

GitHub - davidemms/SHOOT: SHOOT.bio - the phylogenetic search engine

SHOOT.bio - the phylogenetic search engine. Contribute to davidemms/SHOOT development by creating an account on GitHub.

github.com
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Registrations are now open for the 4th edition of the #ComparativeGenomics course with @sedlazeck and Ingo Ebersberger in March 🔗physalia-courses.org/courses… #Genomics #Bionformatics @PacBio #longreads @nanopore
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