alignment-cat(1)

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.