update README.md

README.md

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-# submitFiles
+submitFiles
+===========
+
 Condor submit files (and executable where applicable)
+
+File Descriptions
+=================
+fasttree.submit
+---------------
+This submit file executes the fasttree program from the /opt/PepPrograms folder. The "10" in the arguments line specifies the desired number of threads, while the "dummy_snps.fasta" corresponds to the input file (your snp alignment). 
+
+>condor_submit fasttree.submit
+
+run_parsnp.submit
+-----------------
+This submit file executes a corresponding bash script (run_parsnp.sh) with three arguments: a compressed folder (.tar.gz) containing the genomes to be assembled (fasta format), the path to the reference genome (stored in opt/data), and the number of threads to use.
+
+>condor_submit run_parsnp.submit
+
+run_parsnp.sh
+-------------
+This is a simple bash script that will unpack the compressed genomes, make and move them into a directory, execute parsnp, and finally compress parsnp's output (a folder containing various files) so that it can be transferred back.