Provided by: bali-phy_3.3+dfsg-1_amd64
alignment-thin – Remove sequences or columns from an alignment.
alignment-thin alignment-file [OPTIONS]
Remove sequences or columns from an alignment.
-h, –help Print usage information. -v, –verbose Output more log messages on stderr.
SEQUENCE FILTERING OPTIONS:
–cutoff arg Keep only sequence with more mismatches than arg. –longer-than arg Keep only sequences longer than arg. –shorter-than arg Keep only sequence sequences shorter than arg. –keep arg Keep only sequences in comma-separated list arg. –remove arg Remove sequences in comma-separated list arg. –down-to arg Remove similar sequences down to arg sequences. –remove-crazy arg Remove arg sequences that are missing too many conserved sites. –conserved arg (=0.75) Fraction of sequences that must contain a letter for it to be considered conserved.
COLUMN FILTERING OPTIONS:
–min-letters arg Remove columns with fewer than arg letters. –remove-unique arg Remove insertions in a single sequence if longer than arg letters
–sort Sort partially ordered columns to group similar gaps. –show-lengths Just print out sequence lengths. –find-dups arg For each sequence, find the closest other sequence.
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <email@example.com>.
Benjamin Redelings. Feb 2018 alignment-thin(1)