rewrite docs

README.md

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 # APP-HD-pattern-runner
-Srcipts, input data and settings files for reproducibility - to be used
-with tools in repos [ProteinPatternSearch](https://github.com/ador/ProteinPatternSearch)
-and [PhyTreeSearch](https://github.com/ador/PhyTreeSearch).
+
+This is an auxiliary repository, containing example runner scripts and configuration files
+for the reproducibility of the R&D work presented in 
+Chapter 5 of my [dissertation](https://www.dropbox.com/s/cow9vys7wrl1kqj/thesis_aszabo.pdf?dl=0).
+
+The scripts and configs are to be used together with tools in these 
+repositories:
+- [ProteinPatternSearch](https://github.com/ador/ProteinPatternSearch)
+- [PhyTreeSearch](https://github.com/ador/PhyTreeSearch).