DOKK / manpages / debian 12 / bali-phy / alignment-cat.1.en
alignment-cat(1) alignment-cat(1)

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

alignment-cat file1 [file2 ...]

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

Produce help message
Which output format: fasta or phylip?
Ranges of columns to keep, like: 1-10,30-
Taxa to keep, comma-separated
Add gaps to make sequence lengths identical
Reverse the sequences
Remove columns with no characters (all gaps).
What letters are not characters (e.g. gaps)?
Remove all non-character letters from sequences.
Reorder the sequences given a tree
use the root specified in the tree file to reorder
Reorder the sequences following an alignment
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.

Feb 2018