[EMBOSS] How to switch off fneighbor's "banner"?

Jan Kim jttkim at googlemail.com
Wed Jan 8 22:38:22 UTC 2014

Dear All,

firstly (albeit perhaps a bit belatedly) a Happy New Year to all.

I'm trying to automate the process of constructing a neighbor joining
tree (in the standard Newick format) using fneighbor, and I almost got
there. The command line I arrived at is:

    fneighbor -filter -auto -progress N -treeprint N -printdata N -trout Y -outtreefile stdout

The output this produces is:

    Neighbor-Joining/UPGMA method version 3.69

      10 Populations

     Neighbor-joining method

     Negative branch lengths allowed

followed by the Newick tree I'm after. The only problem is that Newick
parsers don't really expect those initial lines quoted above.

For the time being I've worked around this by reading and discarding the
first 11 lines of output before handing over to the parser. But is there
a more elegant way which I've missed?

Best regards & thanks in advance, Jan
 +- Jan T. Kim -------------------------------------------------------+
 |             email: jttkim at gmail.com                                |
 |             WWW:   http://www.jtkim.dreamhosters.com/              |
 *-----=<  hierarchical systems are for files, not for humans  >=-----*

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