# The `--align` command:

--align <file>                              Sequence data.

Specify a collection of sequences to align in FASTA format.
If this option is given multiple times, each FASTA file should
contain sequences with the same names.  Sequences from each
file form a separate partition and may be described with
different models.

FASTA files are usually specified without the `--align` command:

   bali-phy dna.fasta rna.fasta

This is equivalent to

   bali-phy --align=dna.fasta --align=rna.fasta

The initial alignment for each partition is taken from the
alignment of the sequences in the FASTA file.

# Examples:

   bali-phy dna.fasta
