Circos for comparative genomes

Circos:
nucmer –prefix=refBAV1_qryVScds Dehalococcoides_BAV1.fasta Dehalococcoides_VS.cds.fasta
show-tiling -i 80 -c refBAV1_qryVScds.delta > refBAV1_qryVScds.tiling
awk -F ” ” ‘{print “chr1″ “\t” $1 “\t” $2}’ refBAV1_qryVScds.tiling > Dehalococcoidessp.VScds.gene_tableBAV1.txt

shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/circos/circos-tutorials-0.62/tutorials/8/1$ perl ../../../../circos-0.62-1/bin/circos -conf circos.conf

shenzy@shenzy-ubuntu:/winxp_disk2/shenzy/circos/circos-tutorials-0.62/tutorials/8/1$ ll
total 16001
-rwxrwxrwx 1 root root 528519 2012-12-27 16:11 circos1.png
-rwxrwxrwx 1 root root 1065925 2012-12-27 14:33 circos2.png
-rwxrwxrwx 1 root root 1230394 2013-01-15 14:04 circosBAV1_VS11a_genome.jpg
-rwxrwxrwx 1 root root 4654 2013-01-15 13:11 circos.conf
-rwxrwxrwx 1 root root 1119210 2013-01-15 13:36 circos.jpg
-rwxrwxrwx 1 root root 794858 2013-01-15 13:15 circos.png
-rwxrwxrwx 1 root root 2900177 2013-01-15 13:15 circos.svg
-rwxrwxrwx 1 root root 4242152 2013-01-15 13:32 circos.xcf
-rwxrwxrwx 1 root root 4242152 2013-01-15 13:30 circos.xcf.png
-rwxrwxrwx 1 root root 128 2013-01-14 15:01 highlights.conf
-rwxrwxrwx 1 root root 2075 2013-01-14 14:42 highlights.conf.org
-rwxrwxrwx 1 root root 892 2013-01-15 13:15 ideogram.conf
-rwxrwxrwx 1 root root 35132 2011-03-22 00:40 image-01.png
-rwxrwxrwx 1 root root 30883 2011-03-22 00:40 image-02.png
-rwxrwxrwx 1 root root 126878 2011-03-22 00:40 image-03.png
-rwxrwxrwx 1 root root 1305 2012-05-05 00:25 ticks.conf