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.