Subset filter allows to filter sequences for each block by keeping only a selection of species.
maf.filter= \ [...], Subset( \ species=(species1, species2, etc), \ strict=yes, \ keep=no, \ remove_duplicates=yes), \ [...]
species=(species1, species2, etc)
A coma separated, within parentheses, list of species. Only sequences corresponding to the selected species will be kept. Block without sequences from the selection will be discarded.
If set to yes, only blocks containing at least one sequence from each species in the selection will be kept.
If strict is set to yes, tells if additional sequences should be kept in the block, or remove so that the output blocks only contain species from the selection.
If set to yes, only keep blocks for which only one sequence for each species is present. Blocks with paralogous sequences in at least one species will therefore be discarded.