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From here you may download the entire software suite and associated input files. The README and README_MAC files gives detailed instructions.


README

Linux/Unix Users:

opt-3.19.tar.gz or from here Required options parsing software. Install this first.
cisortho-1.0.tar.gz Source Code distribution. Should compile on most Unices.
cisortho_input.tar.gz 48Mb Compressed Input files, tar archive
hmmer-2.3.2.tar.gz or from here Used to build a Position Weight Matrix from aligned DNA.


Windows (Win32) Users:

cisortho.exe CisOrtho Win32 executable
cis.exe Cis Win32 executable
cisortho_input.zip 48Mb Compressed Input files, zip archive.
hmmbuild.exe hmmbuild Win32 executable (Ported from Sean Eddy's HMMER Source Code)


Mac OSX Users:

cisortho CisOrtho MacOSX terminal application. ( Launch in a terminal. See README_MAC)
cis Cis MacOSX terminal application.
cisortho_input.zip 48Mb Compressed Input files, zip archive.
hmmer-2.3.2.bin.powerpc-apple-osx.tar.gz or from here hmmer-2.3.2 Mac OSX binary

Source Files used to derive Input Files

Note: You only need these if you want to restrict your search to regions other than all non-exonic regions (see Methods).
C. elegans exon annotation GFF files (CHROMOSOME_*.exon.gff) from here.
C. elegans fasta chromosome sequences (CHROMOSOME_*.dna) from here.

The following are direct links:
C. briggsae exon annotation GFF file cb25.hybrid.exons2.00.gff
C. briggsae fasta sequence file cb25.agp8.fasta.gz.
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