alignment-cat(1)

Usage

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:

BAli-Phy online help: ⟨http://www.bali-phy.org/docs.php⟩\c .

Please send bug reports to ⟨[email protected]⟩\c .

4 releases since Debian 10 (Buster); the text changed 2 times.