Version 2.0.5

A new, Python-based implementation of the CLANS software for 3D visualisation of the relationship between proteins, based on their pairwise sequence similarities.
CLANS can be used in two modes:
• GUI-based visualization tool (default mode), which gets a matrix of sequence similarities and
displays them as a dynamic graph using the Fruchterman-Reingold force-directed layout.
In addition to clustering the sequences in space, the visualization tool enables to explore the data in various ways, which include manual interaction with the graph (rotation, panning, zoom-in and out, selection of data-points), different views of the data, several selection options, grouping and coloring the data (or a subset of it) by different features.
• Command-line tool (executed using the ‘-nogui’ flag), which can be used to obtain a matrix of sequence similarities by running all-against-all BLAST search. In addition, it can run the Fruchterman-Reingold force-directed graph layout for a defined number of iterations and save the results in a clans-formatted file which can later be loaded and presented in the visualization tool. This is recommended for large datasets (>5000 sequences, depending on the computer resources), in which the clustering process is slow and there is no advantage in visualizing it.
The BLAST search is only available in the command-line mode.