Fig 1.
Dnaml workflow is used (left part of the figure), DNA sequences are aligned with Clustal Ω and processed by Dnaml, a phylogenetic tree is generated. If the Immcantation workflow is used (right part of the figure), reads are processed through Change-O pipeline and IgPhyML will generate the trees. AncesTree processes the different inputs and reconstructs the phylogenic tree with all information related to Ig. The tree is displayed in a GUI and an Extensible Markup Language (XML) file is produced (that could be used as direct input into AncesTree).
Fig 2.
(A) The tree generated by Dnaml is displayed in the main panel. The BASELINe analysis for the clonal family is displayed in the right upper corner. (B) The mutations between two nodes can be displayed in a separate window and they are positioned using IMGT sequence annotation. (C) The user can have access to each specific node to obtain the related sequences (DNA or protein) and add comments. (D) An alignment is generated with the UCA appearing in the first lane, and a ruler indicates the different regions that compose an Ig sequence.
Fig 3.
Clonal family against F-RSV protein antigenic site V.
(A) Shown is the prefusion conformation of F-RSV trimer (PDB ID: 4MMU) [46]. The antigenic sites are colored, site Ø (red), I (blue), II (yellow), III (green), IV (purple) and V (orange). (B) Table showing the different characteristic of a mAbs clonal family isolated from an infant (≥ 6 months) after RSV infection. The Igs neutralization titers are shown as well as their related Germline annotations. ADI-14576 is highlighted because of is lower neutralization value in comparison to the other mAbs of the same clonal family. Phylogenetic analysis of the VH chain of a clonal family F-RSV specific. (C) Phylogenic tree displayed in AncesTree where the user clicked on the mutation shared by all Igs below BP3 node (31: S->N). (D) Protein alignment of the different Ig sequences, the mutation 31: S->N is boxed.