A suite of phylogenetic tools for reticulate evolution.
SPECTRE provides several new implementations of pre-published algorithms to construct phylogenetic trees and networks (more precisely split networks), along with an interactive graphical interface for visualizing planar split networks. SPECTRE also supports the use of longer running algorithms by providing command line interfaces, which can be executed on servers or in High Performance Computing (HPC) environments.
Different methods have been developed for computing such networks and some of them are implemented in separately as standalone tools or as closed source. This makes it difficult for developers to create new algorithms and customize existing ones. Therefore, I felt there is a need for robust, open-source implementations of associated data structures and algorithms. Additionally, a lot of the implementations of construction algorithms are difficult to install and/or to run, might have several external dependencies and requiring several steps from sequencing data to a publication ready figure. SPECTRE is an open-source software suite and java library, providing an easier way for developers to either extend implemented approaches or create ones from scratch leveraging SPECTREs data structures, algorithms and file format parsing functionality.
