Alignment file in TAB format. The suggested way to obtain it is to run Last and than convert the file from MAF to TAB with maf-convert

Gff file of the query organism. The gene IDs in the GFF must be unique. To solve the problem please extract only the 'gene' lines. Try to format the file with AWK: awk `{if ($3==\'gene\') print $0}` GFFfile

Gff file of the 'target' organism. The gene IDs in the GFF must be unique. To solve the problem please extract only the gene lines as explained in queryGff

Interval, in nucleotide, within a gene is considered in the same position.

Output options. If not specify the software shows only the genes that are in the exact position of the genes in the target. It's possible to show annotated genes that are in aligned regions but that have different lengths or in slightly different positions. It's possible to select multiple values.

This option needs the fasta file of the genome. This will slow down the process A LOT.