Fast DNAml - restart format help!

James McInerney jamm at nhm.ac.uk
Tue Nov 11 11:04:45 EST 1997


Robert,

I think the problem might be the square brackets.  The information that is
surrounded by square brackets is superfluous (at least for this purpose) so
you should remove it.

I think that this is the problem.  Have a go and let me know how you get on.

James

Dr. Robert Rumpf wrote:
> 
> I need to restart a tree being constructed with Fast DNAml, and I can't
> seem to get the file format correct.  I've appended the last line of the
> checkpoint file to the end of my data file, and when I try to run the
> program I get this message:
> 
> Restarting from tree with the following sequences:
> ERROR: Missing '(' at start of tree; End-of-File found instead
> 
> So what does a valid file look like at this point?  Here's the tail end of
> my data set:
> 
> (majority of data not shown)
> -TAAGAAGGC ---------
> -TAAGAAAGC ---------
> -TAAAGAAGC ---------
> -TAAGAG--C ---------
> -TAAGAAAG- ---------
> AA--GGAAGC ---------
> -TAAGAAAG- ---------
> [&&fastDNAml: version = '1.0.6', likelihood = -1599.3774869798162, ntaxa =
> 18, opt_level = 0, smoothed = 1] ('381': 0.000001,('A7A1':
> 0.000001,((('A151': 0.004275,('A39': 0.011690,'FS8': 0.005736): 0.002877):
> 0.000001,(('ESO': 0.004339,'HG1691': 0.005780): 0.001432,((('FS106':
> 0.000001,'W50': 0.000001): 0.000001,('HG445': 0.000001,'17': 0.000001):
> 0.000001): 0.000001,('B57': 0.000001,('17.5': 0.000888,'817': 0.023210):
> 0.000529): 0.001411): 0.002821): 0.001407): 0.000001,('DCR':
> 0.002880,('A62': 0.000001,'A120.17A': 0.060761): 0.007209): 0.000001):
> 0.001414): 0.002840,'77': 0.002844):0.0;
> 

-- 
=========
James O. McInerney               email: J.mcinerney at nhm.ac.uk
Department of Zoology,           phone: +44 171 938 9247
The Natural History Museum,      Fax:   +44 171 938 9158
Cromwell Road,                    
London SW7 5BD.                  
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