Update README.md

README.md

 # nested
 
+#### External tools
+Program is using other external tools. Before usage make sure you have the following tools installed:
+
+- LTR finder (v 1.05+) -
+http://www.mybiosoftware.com/ltr_finder-1-0-5-find-full-length-ltr-retrotranspsons-genome-sequences.html
+- blastx (v 2.2.31+) -
+https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download
+- genometools (v 1.5.8) with gt sketch -
+https://github.com/genometools/genometools
+
+#### Python3 libraries
+Program is running only on Python 3 version and uses non-standard libraries:
+
+- BioPython -
+http://biopython.org/
+- BCBio GFF -
+https://github.com/chapmanb/bcbb/tree/master/gff
+- networkx -
+https://networkx.github.io/
+
+#### Setting up the config
+Before usage, **python/config.py** needs to be set up:
+
+- ltr paths - executable, prosite and tRNAdb
+- ltr arguments 
+- gt sketch path
+- gt sketch arguments
+- blastx protein database (our database available at ... )
+- blastx arguments
+
 ```
 Usage: python3 main.py [OPTIONS]