SEQUENCE BUNDLES

ABOUT ALVIS

ALVIS is an open-source software tool developed in a collaboration between the Goldman Group at EMBL-EBI and Science Practice. ALVIS integrates a suite of interactive visualisation tools including Sequence Bundles with a set of explorative computational tools including phylogenetic and correspondence analyses.

Go to ALVIS repository to download the binary release that is ready to use, or clone the repository to work with source files. ALVIS is open and free software released under GNU Affero General Public License version 3. You are welcome to use and contribute to ALVIS in academic, commercial, and non-commercial work. Please cite:

ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments. RF Schwarz, AU Tamuri, M Kultys, J King, J Godwin, AM Florescu, J Schultz and N Goldman.
Nucleic Acids Research (05 May 2016) 44 (8): e77

and

Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs. M Kultys, L Nicholas, R Schwarz, N Goldman, J King.
BMC Proceedings 2014, 8 (Suppl 2): S8

FEATURES AND REQUIREMENTS

Selected ALVIS features:

• Sequence Bundles visualisation
• Extensive suite of interactive visualisation tools
• Numerical analysis (dimension reduction, classification)
• Detection of covariant sites
• Detection of motifs
• Generation of phylogenetic trees
• Annotation of trees with synapomorphies and homoplasies
• Manual and programmatic clustering of sequences
• Export of publication-quality visualisations
• Saving projects (data and workspace settings embedded)
• High workspace customisability

ALVIS works on both Windows and Mac OS computers.
Software requirements:

• Java 7 (update 67 or later)
• Approx. 200MB disk space
• Minimum 2GB RAM (4GB recommended)
• For advanced features: R with rJava and "kernlab" package