DODO takes protein sequences as input. The protein sequences should be prepared in FASTA format and separated into different file according to their species. These FASTA files should be named as "species_name.fasta".

After decompressing DODO.tar.gz, there is a file named "Setting.txt".

cddDir: The path of domain database used in rpsblast step. Default set is pfam23 database which has already been included in the DODO.tar.gz file.

ProjectFolder: All intermediate files will be generate under this folder.

ReferenceGenome: reference genome used in DODO

BlastProgram: the path to the blast executable

OutputFile: orthologous relationships record in this OutputFile

An example:

output file

The output file is a text file separate by tabs and looks like this:

The first column is Ortholog group ID given by DODO. There are two kind of ortholog groups. Ortholog group ID having No_DomainInfo as prefix are ortholog groups of no domain protein sequences identified solely from reciprocal best hits. Ortholog group ID starts with PfamArcNu are proteins identified aided by domain information and reciprocal best hits. The second column is the species name (the file names of FASTA files) and the third column is the gene name.