Home

Overview
(Note: this is a protype tool and further details will be provided if development continues. The protype however is usable in its current form and might be of use for some types of sequence visualization).

TreeScope is a tool that increases the ease of rapidly interacting with sequence data at a highly detailed level. In this protype once the alignment has been loaded interactive trees can be readily created across various user selected section. Trees can be used to identify clusters from which nucleotide and amino acid frequencies can be easily, and immediately, extracted. Future developments will involve including recombination detection strategies using phylogenetic approaches as well as statistically comparing divergence rates across trees from different regions. At the moment an executable jar is available for download as well as some screenshots. Code will be made available on publication.

See the first draft of the [Help Manual] to get started.

Software Developer: John Archer

I have been working on code for TreeScope on and off since 2022. The idea came from software (CView) I created as a small part of an earlier FCT funded project. In many ways TreeScope can be seen as a much improved (or version 2) of CView. During 6 months of 2025 I was kindly hosted by the IMED group within CIBIO after my on small group finally ended. During that time I continued to work on TreeScope within the group with some kind advice and pointers from members within and outside of the group including:

Pedro Esteves: Group Leader of IMED
Joana Abrantes: Researcher within IMED
Ana Margarida Lopes,: Researcher within IMED
James Harris: Group leader of Applied Phylogenetics
Raquel Linheiro: Research on CView software
Stephen Sabatino: Research on CView software

Licence and Disclaimer

This software is free and open-source software released under the GNU General Public License (GPL).

The software is provided "as is" and without warranty. It may contain errors or produce incorrect results. Users are responsible for evaluating the software and independently verifying any results before relying upon them, particularly for scientific, medical, or other consequential purposes.

To the extent permitted by applicable law, the author accepts no liability for any loss, damage, or other consequence arising from the use of this software.

Java Runtime

The software is intended to run on OpenJDK or another freely available Java Runtime Environment (JRE) or Java Development Kit (JDK) providing the required Java functionality. Compatibility may vary between Java versions and implementations. Third-party libraries or data included with or used by the software may be subject to their own licences and conditions.