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README.md

Example / Tutorial

Test set

  • 14 proteome data used obtained from NCBI refseqDB which are enlisted in "16_items_list.ods" and "16_items_list.xlsx"
  • 2 random proteomes generated by shuffling each protein's sequence order in proteome. The original proteomes obtained from Mycocosm DB, Joint Genome Institute (JGI)
  • "Tutorial_16_proteomes" contains 5 Ascomycota, 5 Basidiomycota, 3 Protists, 1 Monokaryote, and 2 randoms

Follow

1. Run FFP Profiler

  • Input is proteome (amino acids), -a
  • Feature length (l-mer) is 13, -s 13
  • Normalize output (frequency), -n
  • Output folder is "./FFP_13", manually created

./FFP_compress -a -s 13 -n 931890 ./FFP_13/931890
./FFP_compress -a -s 13 -n 332648 ./FFP_13/332648
./FFP_compress -a -s 13 -n 367775 ./FFP_13/367775
./FFP_compress -a -s 13 -n 418459 ./FFP_13/418459
./..
./..
./..
./FFP_compress -a -s 13 -n R990650 ./FFP_13/R990650

2. Run JSD Calculator

  • Using 3 threads, -t 3
  • Standard output to "16_items_13.matrix", is a symmetric matrix using [-s]

./JSD_maxtrix -s -t 3 ./FFP_13/* > 16_items_13.matrix

  • Sample output: "16_items_13.matrix" (the symmetric matrix input for BIONJ input)

3. Construct a tree (newick) from the divergence matrix

  • You can use either BIONJ or NJ. However, BIONJ requires to input a symmetric matrix
  • For this example, we use BIONJ provided here (http://www.atgc-montpellier.fr/bionj/) but any method that takes distance/divergence matrix works

./BIONJ 16_items_13.matrix 16_items_tree.newick

  • Sample output: "16_items_tree.newick"

4. Tree Visualization

Workflow

  • Repeat the "Follow" cycle above per feature length (l-mer) and tree
    Workflow