NAME

       alignment-cat - Concatenate several alignments (with the same sequence names) end-to-end.

SYNOPSIS

       alignment-cat file1 [file2 ...]

DESCRIPTION

       Concatenate several alignments (with the same sequence names) end-to-end.

ALL OPTIONS:

       -h, --help
              Produce help message

       --output arg (=fasta)
              Which output format: fasta or phylip?

       -c arg, --columns arg

              Ranges of columns to keep, like: 1-10,30-
       -t arg, --taxa arg
              Taxa to keep, comma-separated

       -p, --pad
              Add gaps to make sequence lengths identical

       -r, --reverse
              Reverse the sequences

       -e, --erase-empty-columns
              Remove columns with no characters (all gaps).

       --missing arg (=-?)
              What letters are not characters (e.g.  gaps)?

       --strip-gaps
              Remove all non-character letters from sequences.

       --reorder-by-tree arg
              Reorder the sequences given a tree

       --use-root
              use the root specified in the tree file to reorder

       --reorder-by-alignment arg
              Reorder the sequences following an alignment

       --align-by-amino arg
              Arrange nucleotides into codon alignment

EXAMPLES:

       To select columns from an alignment:

              % alignment-cat -c1-10,50-100,600- filename.fasta > result.fasta
              % alignment-cat -c5-250/3 filename.fasta > first_codon_position.fasta
              % alignment-cat -c6-250/3 filename.fasta > second_codon_position.fasta

       To concatenate two or more alignments:

              % alignment-cat filename1.fasta filename2.fasta > all.fasta

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-cat(1)