table of contents
| alignment-cat(1) | 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.| Feb 2018 |