Fast DNAml - restart format help!

Dr. Robert Rumpf rrumpf at postbox.acs.ohio-state.edu
Mon Nov 10 13:37:57 EST 1997


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;

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