# The `--name` command:

-n     <name>                               Name for output directory.
--name <name>

BAli-Phy avoids over-writing output from previous runs by
creating a new directory for each run to contain output files.

If the run is named `<name>`, BAli-Phy attempts to create `<name>-1`,
`<name>-2`, etc. until it finds one that does not already exist.

If the <name> is not given, the input-file names are concatenated
to construct a name.

The `<name>` is allowed to contain directory separators `/`. Thus
`--name=hi/there` will create the directory `hi/there-1`.  The
directory `hi` will also be created if it does not exist.

# Examples:

   bali-phy dna.fasta aa.fasta --name combined

   bali-phy dna.fasta aa.fasta --name project/combined
  
   bali-phy dna.fasta aa.fasta --name /home/self/project/combined
