Running:

• java -jar DGraph.jar

Example usage:

1. Make distance graph from short peptides or already-aligned sequences

• Input: Fasta file
• Choose "Run DGraph"
• Choose "Generate PD scores" and check "PD score for aligned sequences"
• Onscreen instructions say how to adjust the figure generation.
• Press 's' to generate a PDF + PNG of the output

2. Make distance graph from unaligned sequences (Sliding window approach)

• Input: Fasta file
• Choose "Run DGraph"
• Choose "Generate PD scores." (Optionally) change the window size.
• Onscreen instructions say how to adjust the figure generation.
• Press 's' to generate a PDF + PNG of the output

3. Make distance graph from unaligned sequences (Alignment approach)

• Input: Fasta file
• Run clustalw, i.e. from https://www.genome.jp/tools-bin/clustalw
• Download the .aln file. (Optional) Copy+paste full clustalw output to file.
• Run jalview and convert the .aln to a fasta of sequences with dashes
  • Note: To do this, open the .aln in jalview, Ctrl+A then Ctrl+C.
  • Then, in a text editor Ctrl+V to paste the Fasta of the alignment
• Now continue with the example 1, using this new fasta file.

How to generate input files:

• Dgraph supplies a number of utilities for getting input into a usable format.
• "Coloring" file format: Readme TODO

Running in a script:

• Run java -jar DGraph.jar -Dhelp to see a list of batch processing options.

Compiling from source

• Depends on core.jar, itext.jar, and pdf.jar from Processing-1.5.1, which can be found here:
  • https://github.com/processing/processing/releases/tag/processing-1.5.1