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Frederic Lemoine

@fredebibs

Bioinformatics @institutpasteur ; data science, ngs, transcriptomics, biotech, evolution, phylogeny,... golang
Paris, France Joined March 2009
835 Following 723 Followers 529 Posts

Latest posts 5

Frederic Lemoine @fredebibs
Our recently published study in PLoS Computational Biology introduces DIPScan, a method to identify deletion-containing viral genomes in sequencing data and correct consensus genomes that might otherwise include erroneous mutations doi.org/10.1371/journa…
journals.plos.org Accounting for Defective Viral Genomes in viral consensus genome reconstruction, application to... Author summary Over the past few years, viral genome sequencing has become a cornerstone of epidemic surveillance, and generating accurate consensus viral genomes is essential for this effort....
Frederic Lemoine @fredebibs
PhyML now implements the Bayesian phylogenetic bootstrap! To test it: option "--bayesian_bootstrap" with the latest commits of PhyML: github.com/stephaneguindo…
Example: `phyml -d nt -i align.phy -m GTR -b 100 --bayesian_bootstrap`
github.com GitHub - stephaneguindon/phyml: PhyML -- Phylogenetic estimation using (Maximum) Likelihood PhyML -- Phylogenetic estimation using (Maximum) Likelihood - stephaneguindon/phyml
Frederic Lemoine @fredebibs Nov 9, 2024
This is now published in @MolBioEvol ,
Thanks to the reviewers who helped improve the manuscript!

doi.org/10.1093/molbev…
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Frederic Lemoine @fredebibs
Accounting for partner notification in epidemiological birth-death models medrxiv.org/content/10.110…
www.medrxiv.org Accounting for partner notification in epidemiological birth-death models Phylodynamics bridges the gap between classical epidemiology and pathogen genome sequence data by estimating epidemiological parameters from time-scaled pathogen phylogenetic trees. The models used...
Frederic Lemoine @fredebibs
"Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping to evade (Over-)optimization". Faster tree inference in RAxML-NG biorxiv.org/content/10.110…
www.biorxiv.org Much Ado About Nothing: Accelerating Maximum Likelihood Phylogenetic Inference via Early Stopping... Maximum Likelihood (ML) based phylogenetic inference constitutes a challenging optimization problem. Given a set of aligned input sequences, phylogenetic inference tools strive to determine the tree...
Frederic Lemoine @fredebibs
Our new preprint: « The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches »
biorxiv.org/content/10.110…
In this approach, bootstrap MSA sites are given continuous weights rather than being sampled with replacement.
www.biorxiv.org The Bayesian Phylogenetic Bootstrap, Application to Short Trees and Branches Felsenstein’s bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result in massive sampling of taxa (e.g. SARS-CoV-2). In this...