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:

--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

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.

REPORTING BUGS:

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

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