Tree comparison & consensus

• Consensus network - Consensus network from multiple trees

• Consensus tree - Consensus tree from multiple trees

• Cophylogenetic plot (tanglegram) - Tanglegram for comparing two trees

• Evolutionary tempo mapping - Detect rate-topology associations in gene trees

• Kuhner-Felsenstein distance - Branch score distance between trees (topology + branch lengths)

• NeighborNet - NeighborNet phylogenetic network from distance matrix (Bryant & Moulton 2004)

• Polytomy testing - Test for polytomies in a tree

• Quartet network - Quartet-based network visualization

• Quartet pie chart - Phylogram with quartet concordance pie charts at internal nodes

• Robinson-Foulds distance - Topological distance between trees

• Spectral discordance decomposition - PCA ordination and clustering of gene tree topologies

• Tree space visualization - Visualize gene tree topology space via MDS, t-SNE, UMAP, or clustered distance heatmap