Provided by: bali-phy_3.3+dfsg-1_amd64 bug

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>.

AUTHORS

       Benjamin Redelings.

                                             Feb 2018                           alignment-thin(1)