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.
-
-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 <
[email protected]>.
Benjamin Redelings.