From BITS wiki
Dotplot is a kind of graph used to compare two sequences. The two basic parameters are window size and treshold. It is a convenient and rapid method to compare long DNA or protein sequences for similarity
Software to create dot plots
- EMBOSS contains the programs
- dottup : word comparison
- dotmatcher : window/threshold comparison
- dottup : word comparison, makes n*n dotplots in one graph
- Dotter: developed by Erik Sonnhammer and Richard Durbin (U. Stockholm, Sweden)
- Dotlet (Java applet) at the Swiss Institute of Bioinformatics
- Gepard (Munich Information center for Protein Sequences, Germany) : with heuristic for speeding up computation, for comparing very long sequences
- YASS: DNA pairwise alignment tool.
- JDotter - Originally developed for viral genomes - JAVA - Very powerful with a lot of options!
- MUMmer - Aligning genomes, with inclusion of dotplot capabilities.
- UGene - A complete sequence analysis platform with integrated dotplot viewer.
- MAUVE - A GUI available for the three main OS.