alignment-cat

alignment-cat file1 [file2 ...]

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

-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

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
    

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

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

Benjamin Redelings.