Input
Nucleotide sequence	Nucleotide FASTA-file with a single genomic sequence (without gaps).
Protein set	MultiFASTA-file with protein sequences, without gaps. Headers can include additional information in Softberry AbInitio or FGENESH++ format. Here IPI or NR database could be given on input.
Output
Output file	Specially formatted file with the pseudogenes descriptions. Fields are separated with '@@' sequence. List of fields: chr chromosome (or another sequence) name is which search has been carried out chain chain pos(dir.ch.) (nt.) pseudogene start position (in direct chain) len(nt.) (nt.) pseudogene length. Note thate pseudogene lies from the right of 'pos(dir.ch)' identity (%) Identity with a protein (0...100%). coverage (%) Coverage of a protein with alignment Ka/Ks ratio calulated by Nei-Gojobori method uali.head (yes/no) first codon of alignment is ATG uali.tail (yes/no) last codon of alignment is stop-codon exons#,lower number of exons, lower estimation exons#,upper number of exons, upper estimation polyA (yes/no) there is a polyA tail at the 3' terminus of alignment polyA_signal (yes/no) there is a polyA signal at the 3' terminus of alignment corr.stops# number of correctable (by one mismatch) in-frame stop codons uncorr.stops# number of uncorrectable (by one mismatch) in-frame stop codons corr.frameshifts# number of correctable (by one-nucleotide instertion/deletion) frameshifts uncorr.frameshifts# number of incorrectable (by one-nucleotide instertion/deletion) frameshifts prototype_chr chromosome of prototype protein gene prototype_prot_name prototype protein gene name prototype_exon#,lower number of exons of prototype prot. gene, lower estimation prototype_exon#,upper number of exons of prototype prot. gene, upper estimation DNA_identity Identity between prototype gene and pseudogene at the level of DNA CDS length (nt.) CDS length