Jeremy recently organized and taught a workshop on TreeScaper, software that he helped develop, for the Society of Systematics Biologist Conference in Baton Rouge, Louisiana.
TreeScaper provides a collection of visual and quantitative tools for exploring and characterizing sets of binary trees with an emphasis on phylogenetic trees.
These tools can be broadly categorized into three types:
1. Utilities for calculating basic information about topologies and bipartitions
2. Visualization of treespace in 2- or 3-dimensions through non-linear dimensionality reduction
3. Detection and delineation of distinct ‘communities’ within a tree network using a graph-theoretic approach known as community detection.
Though we have focused our tools on binary trees, they can analyze any data for which a distance matrix can be constructed.
All workshop materials including multiple tutorials can be found here. You can also read the paper here.