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 <i>et al</i>. (<i>DOI will be linked at a later date</i>).The original input file (<i>'Sornberger2025.fasta'</i>) 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 (<i>'augur-align-Sornberger2025.fasta'</i>). A maximum-likelihood tree was built using the IQ-TREE method and rooted to the germline gene (<i>'augur-tree-Sornberger2025.nwk'</i>). The tree was refined (<i>'augur-refined-Sornberger2025.nwk'</i>), visualized using the Auspice toolkit (<i>'auspice-input-Sornberger2025.json'</i>), and colored in Adobe Illustrator (resultant trees can be found in Supplemental Figures).