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

-h, –help
              Produce help message

       –outputarg (=fasta)
              Which output format: fasta or phylip?

       -carg, –columnsarg

              Ranges of columns to keep, like: 1-10,30-
       -targ, –taxaarg
              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).

       –missingarg (=-?)
              What letters are not characters (e.g. gaps)?

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

       –reorder-by-treearg
              Reorder the sequences given a tree

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

       –reorder-by-alignmentarg
              Reorder the sequences following an alignment

       –align-by-aminoarg
              Arrange nucleotides into codon alignment

       Benjamin Redelings.

                                                    Feb 2018                                    alignment-cat(1)

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

       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

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

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

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

alignment-catfile1 [file2 ...]