alignment-thin(1)

Benjamin Redelings

Feb 2018

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:

--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

OUTPUT OPTIONS:

--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.

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

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

REPORTING BUGS:

BAli-Phy online help: http://www.bali-phy.org/docs.php.

Please send bug reports to bali-phy-users@googlegroups.com.