Sornberger 2025 - Phylogenetic Tree Sequences

These files contain all the necessary sequences and information necessary to replicate the phylogenetic trees found in Supplemental Figures 4, 5B, and 6 of Sornberger et al. (DOI will be linked at a later date). The original input file ('Sornberger2025.fasta') contains the sequences of all recombinantly expressed monoclonal antibodies (mAbs), related antibodies using the same heavy-chain variable gene sequence (with ≥ 80% nucleotide sequence identity in the HCDR3), and the germline variable gene (IGHV1-18). The Augur toolkit was used to align all sequences with the somatically mutated candidate mAb FluA-173 using the MAFFT method ('augur-align-Sornberger2025.fasta'). A maximum-likelihood tree was built using the IQ-TREE method and rooted to the germline gene ('augur-tree-Sornberger2025.nwk'). The tree was refined ('augur-refined-Sornberger2025.nwk'), visualized using the Auspice toolkit ('auspice-input-Sornberger2025.json'), and colored in Adobe Illustrator (resultant trees can be found in Supplemental Figures).