TreeGraph 2 is a user-friendly, fully documented application for creating high-quality phylogenetic tree figures. It allows the combination and visualization of evidence from different phylogenetic analyses, enabling users to compare and graphically present incongruent results. The software supports various data formats, including Newick, Nexus, and phyloXML, and can import annotations from text files. It provides flexible editing and formatting options, such as automatically setting branch widths or colors based on node or branch data. Users can also manually construct trees or copy clades from other files. TreeGraph 2 outputs graphic formats like SVG, PDF, and PNG, suitable for publication and presentations. It offers advanced features for visualizing statistical support, ancestral character states, and other annotations. The software is compared favorably to other tree editors, offering unique capabilities such as combining annotations from different analyses and automatically positioning labels. TreeGraph 2 is written in Java and is platform-independent, with extensive documentation and online help. It is particularly useful for researchers working with complex gene family datasets and multiple phylogenetic analyses. The software is available for free under the GNU General Public License.TreeGraph 2 is a user-friendly, fully documented application for creating high-quality phylogenetic tree figures. It allows the combination and visualization of evidence from different phylogenetic analyses, enabling users to compare and graphically present incongruent results. The software supports various data formats, including Newick, Nexus, and phyloXML, and can import annotations from text files. It provides flexible editing and formatting options, such as automatically setting branch widths or colors based on node or branch data. Users can also manually construct trees or copy clades from other files. TreeGraph 2 outputs graphic formats like SVG, PDF, and PNG, suitable for publication and presentations. It offers advanced features for visualizing statistical support, ancestral character states, and other annotations. The software is compared favorably to other tree editors, offering unique capabilities such as combining annotations from different analyses and automatically positioning labels. TreeGraph 2 is written in Java and is platform-independent, with extensive documentation and online help. It is particularly useful for researchers working with complex gene family datasets and multiple phylogenetic analyses. The software is available for free under the GNU General Public License.