Provided by: bali-phy_3.4.1+dfsg-2_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:
--protect arg Sequences that cannot be removed (comma-separated). --remove arg Remove sequences in comma-separated list arg. --longer-than arg Remove sequences not longer than arg. --shorter-than arg Remove sequences not shorter than arg. --cutoff arg Remove similar sequences with #mismatches < cutoff. --down-to arg Remove similar sequences down to arg sequences. --remove-crazy arg Remove arg outlier sequences -- defined as 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.
Remove columns without a minimum number of letters: % alignment-thin --min-letters=5 file.fasta > file-thinned.fasta Remove sequences by name: % alignment-thin --remove=seq1,seq2 file.fasta > file2.fasta Remove short sequences: % alignment-thin --longer-than=250 file.fasta > file-long.fasta Remove sequences with <= 5 differences from the closest other sequence: % alignment-thin --cutoff=5 file.fasta > more-than-5-differences.fasta Like --cutoff, but stop when we have the right number of sequences: % alignment-thin --down-to=30 file.fasta > file-30taxa.fasta Remove dissimilar sequences that are missing conserved columns: % alignment-thin --remove-crazy=10 file.fasta > file2.fasta Protect some sequences from being removed: % alignment-thin --down-to=30 file.fasta --protect=seq1,seq2 > file2.fasta
BAli-Phy online help: <http://www.bali-phy.org/docs.php>. Please send bug reports to <firstname.lastname@example.org>.
Benjamin Redelings. Feb 2018 alignment-thin(1)