NAME

alignment-thin - Remove sequences or columns from an alignment.

SYNOPSIS

alignment-thin alignment-file [OPTIONS]

DESCRIPTION

Remove sequences or columns from an alignment.

GENERAL OPTIONS:

-h, --help
Print usage information.
-V, --verbose
Output more log messages on stderr.

SEQUENCE FILTERING OPTIONS:

-p arg, --protect arg
Sequences that cannot be removed (comma-separated).
-k arg, --keep arg
Remove sequences not in comma-separated list arg.
-r arg, --remove arg
Remove sequences in comma-separated list arg.
-l arg, --longer-than arg
Remove sequences not longer than arg.
-s arg, --shorter-than arg
Remove sequences not shorter than arg.
-c arg, --cutoff arg
Remove similar sequences with #mismatches < cutoff.
-d arg, --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:

-K arg, --keep-columns arg
Keep columns from this sequence
-m arg, --min-letters arg
Remove columns with fewer than arg letters.
-u arg, --remove-unique arg
Remove insertions in a single sequence if longer than arg letters
-e, --erase-empty-columns
Remove columns with no characters (all gaps).

OUTPUT OPTIONS:

-S, --sort
Sort partially ordered columns to group similar gaps.
-L, --show-lengths
Just print out sequence lengths.
-N, --show-names
Just print out sequence lengths.
-F arg, --find-dups arg
For each sequence, find the closest other sequence.

EXAMPLES:

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
    
% alignment-thin --keep=seq1,seq2   file.fasta > file2.fasta
Remove short sequences: 
% alignment-thin --longer-than=250 file.fasta > file-long.fasta
Remove similar sequences with <= 5 differences from the closest other sequence: 
% alignment-thin --cutoff=5 file.fasta > more-than-5-differences.fasta
Remove similar sequences until 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
    
% alignment-thin --down-to=30 file.fasta --protect=@filename > file2.fasta

REPORTING BUGS:

BAli-Phy online help: <http://www.bali-phy.org/docs.php>.
Please send bug reports to <[email protected]>.

AUTHORS

Benjamin Redelings.