Tried and Tested Plotting Tools
Gepard
- Performs iterative sequential alignment followed by Dotplot rendering behind the scenes.
- Can be automated with gepardcmd; however, outputs from the command line are displayed in a GUI interactive style - zoom option prevalent but zoom factor must be specified.
- In addition to internal memory requirements, it is also constrained by the maximum allowable Java Heap space for memory requirements to run since the application is developed in Java
- Slow and computationally expensive - Java Heap runs out of memory and automatically stops compilation after a few hours
DotPlot
- Developed natively in Python3 and can be accessed and installed through PyPI's package collections website.
- Can accept multiple input formats and display output in either GUI mode (Matplotlib) or other formats.
- Options to adjust the window size on which plots are displayed, and show/remove lengthy sequences from axes for better readability/visual appeal.
- Highly memory intensive and slow - requires >180GB to parse and plot on >1GB fasta.
Flexidot
- Older plotting tool with annotative capabilities.
- Only runs on Python version 2.7 and an older version of MatPlotlib, thus not feasible for this project.
DGenies
- GUI style web-tool to render dotplots on multiple FASTA files.
- Cannot process FASTA files >1GB