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This filter removes highly variable regions and split the blocks accordingly. It uses a sliding windows, and compute the entropy for each site in the window. The window is then discarded if it containes more than ’p’ sites with an entropy higher that a user-specified threshold. The alignment block is then split into separate block accordingly.
maf.filter= \
[...],
EntropyFilter( \
species=(species1,species2,etc), \
window.size=10, \
window.step=1, \
max.ent=0.2, \
max.pos=3, \
missing_as_gap=yes, \
ignore_gaps=yes, \
file=data.trash_ent.maf.gz, \
compression=gzip), \
[...]
|
species=(species1, species2, etc)A coma separated, within parentheses, list of species. All calculations will be performed on the sub-alignment corresponding to these species only.
window.size={int>0}The width, in bp, of the sliding window.
window.step={int>0}The step by which the window is moved, in bp.
max.ent={float}The maximum entropy allowed at each site.
max.pos={int>0}The maximum number of positions with an entropy higher than the given threshold.
missing_as_gap={yes/no}Tell if unresolved characters should be counted as gaps.
ignore_gaps={yes/no}Tell if gaps should not be counted in entropy calculation. If no, then gaps are counted as a “fifth” state.
file={none|{path}}An optional file were removed alignment parts will be stored, in the MAF format. This can be helpful for visual inspection and fine tuning of the filter parameters.
compression={none|gzip|zip|bzip2}Compression format for output file (if file != none).