Af_PLM_dataframe        Function to create a dataframe of the Protein
                        Language Model probabilities and ranks of the
                        mutations along the edges of B cell lineage
                        trees.
Af_add_node_feature     Function to add node features to an
                        AntibodyForests-object
Af_build                Function to infer B cell evolutionary networks
                        for all clonotypes in VDJ dataframe as obtained
                        from the 'VDJ_build()' function.
Af_cluster_metrics      Function to make a grouped boxplot of metrics
                        from clusters of clonotypes
Af_cluster_node_features
                        Function to create a barplot of the cluster
                        composition of selected features from each tree
                        in an AntibodyForests-object
Af_compare_PLM          Function to compare the distributions of the
                        Protein Language Model probabilities or ranks
                        of the mutations along the edges of B cell
                        lineage trees across repertoires using the
                        Jensen-Shannon divergence.
Af_compare_across_repertoires
                        A function to compare dynamics of B cell
                        evolution across different repertoires.
Af_compare_methods      Function to compare trees created with
                        different algorithms from the same clonotype.
Af_compare_within_repertoires
                        Function to compare tree topology of B cell
                        lineages
Af_distance_boxplot     Function to make a grouped boxplot of distance
                        between nodes from specific groups and the
                        germline of lineage trees constructed with
                        AntibodyForests.
Af_distance_scatterplot
                        Function to scatterplot the distance to the
                        germline to a numerical node feature of the
                        AntibodyForests-object
Af_edge_RMSD            Function to calculate the RMSD between
                        sequences over each edge in the AntibodyForest
                        object
Af_get_sequences        Function to get the sequences from the nodes in
                        an AntibodyForest object
Af_metrics              Function to calculate metrics for each tree in
                        an AntibodyForests-object
Af_node_size_boxplot    Function to make a grouped boxplot of the
                        normalized average node sizes (number of cells
                        with the exact same sequence) from specific
                        groups of lineage trees constructed with
                        AntibodyForests.
Af_plot_PLM             Function to create a distribution plot of the
                        Protein Language Model probabilities and ranks
                        of the mutations along the edges of B cell
                        lineage trees.
Af_plot_PLM_mut_vs_cons
                        Function to create a boxplot of the Protein
                        Language Model probabilities
Af_plot_tree            Plots lineage tree of clonotype from
                        AntibodyForests object
Af_sync_nodes           Function to synchronize the node labels/names
                        of all clonotypes within all samples of two
                        AntibodyForests objects.
Af_to_newick            Saves an AntibodyForests-object into a newick
                        file
PLM_dataframe           Small PLM dataframe for function testing
                        purposes
VDJ_3d_properties       Function to calculate 3D-structure propoperties
                        such as the average charge and hydrophobicity,
                        pKa shift, free energy, RMSD of PDB files and
                        add them to an AntibodyForests-object
VDJ_import_IgBLAST_annotations
                        Function to import the annotations and
                        alignments from IgBLAST output into the VDJ
                        dataframe.
VDJ_integrate_bulk      A function to integrate bulk and single cell
                        data
VDJ_to_AIRR             Function to convert VDJ dataframe into an
                        AIRR-formatted TSV file.
af_default              Small AntibodyForests object with default
                        algorithm for function testing purposes
af_mst                  Small AntibodyForests object with MST algorithm
                        for function testing purposes
af_nj                   Small AntibodyForests object with NJ algorithm
                        for function testing purposes
calculate_GBLD          Calculate the GBLD distance between trees in an
                        AntibodyForests object. Code is derived from
                        https://github.com/tahiri-lab/ClonalTreeClustering/blob/main/src/Python/GBLD_Metric_Final.ipynb
                        Farnia, M., Tahiri, N. New generalized metric
                        based on branch length distance to compare B
                        cell lineage trees. Algorithms Mol Biol 19, 22
                        (2024).
                        https://doi.org/10.1186/s13015-024-00267-1
compare_repertoire      Example output from
                        Af_compare_within_repertoires() for function
                        testing purposes
igraph_to_phylo         Converts an igraph network into a phylogenetic
                        tree as a phylo object.
newick_to_Af            Converts files with phylogenetic trees in
                        newick format into an AntibodyForests object.
small_af                Small AntibodyForests object for function
                        testing purposes
small_vdj               Small VDJ dataframe for function testing
                        purposes
