We just released the first public version of FlexiDot:
FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and relaxed handling of mismatches and ambiguous residues. The custom shading modules facilitate dotplot interpretation and motif identification by adding information on sequence annotations and sequence similarities to the images. Combined with collage-like outputs, FlexiDot supports simultaneous visual screening of a large sequence sets, allowing dotplot use for routine screening.
Some FlexiDot features:
- handling of error-prone SMRT reads and ambiguity-containing consensus sequences (e.g. derived by alignment or assembly).
- integration of descriptive information on the analyzed sequences (e.g. gff3-type structural sequence annotation or pairwise identities)
- similarity shading modes
- high flexibility for customization and automation
- output as vector and raster graphics
- self, pairwise and all-against-all visualizations
See for example this tutorial on adding gff3-type annotation to a dotplot.
Code, examples and documentation on github: http://github.com/molbio-dresden/flexidot
Publication: K. M. Seibt, T. Schmidt, and T. Heitkam (2018) "FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses". Bioinformatics, in press, http://doi.org/10.1093/bioinformatics/bty395
(Preprint: Latex version at Overleaf)