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
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