Phylograph

Phylograph is a multifunctional phylogenetic tree editor, specially designed for large trees (up to 1000–1200 leaves). It allows building, visualizing, and editing trees in different layouts in an interactive and very intuitive way, using only the mouse.

Tree visualization
• Supports trees in common formats: Newick, Nexus, including bootstrap values and distances.
• Displays different layouts: rectangular, slanted, and radial/unrooted.
• Allows easy rotation, inversion, and branch expansion/compression.
Interactive editing
• Selection, hiding, or movement of nodes and subtrees using the mouse.
• Insertion of labels, OTU grouping, and additional annotations (distances, bootstrap, hosts, URLs).
• Ability to cut branches and add decorations such as brackets, boxes, and arrows.
Export and saving
• Save projects as re-editable files.
• Export graphics in PNG, PostScript, or HTML (with imagemap and OTU-linked areas).
• Visual customization: selection of fonts, colors, and styles for nodes and labels.

• Rooted trees: 4 variants of cladograms (rectangular with/without distances, slanted).
• Radial trees: Optimized algorithm by Bachmaier et al. (2005), adjusting the spacing between small and large subtrees using the equal distant wedges method.
• Allows re-rooting using either a node or an entire branch as an outgroup.

Llorens C, Futami R, Vicente-Ripollés M, and Moya A. 2008. Phylograph: A multifunction java editor for handling phylogenetic trees.In Biotechvana Bioinformatics, SOFT: Phylograph