Run 0_start_pilot.sh

If there is no rdp file, we have to run rdp first. It is in the 0_start_pilot.sh.

First, check parse_read file and see filename and change the path.
Second, check generate_summary_table and pick right info.
third, check parse_metadata file and check "NOTE"
fourth, create a folder which is called "MSA"
fifth, check 0_start_pilot.sh and run each script
sixth, check AAG.fasta file is there or not

1. ./create_rank_result.sh
2. perl parse_metadata.pl
3. perl generate_summary_table.pl
4. sh generateTop10.sh
5. generate_gensum_gencount.pl
6. perl gen_seq_unifrac.pl
7. sh run_clustraw.sh------before run this script, cat RDP/* >> allseqs_rdp.txt

After we will see .phy files in the MSA folder, we use
/scratch/cc0430/phylip-3.69/src/dnadist and copy the filename on it and type "y"
mv outfile idealSeqs.0.6.fasta.dnadist.outfile
/scratch/cc0430/phylip-3.69/src/neighbor and take idealSeqs.0.6.fasta.dnadist.outfile and type "y"
mv outfile idealSeqs.0.6.fasta.neighbor.outfile
mv outtree idealSeqs.0.6.fasta.neighbor.outtree