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)