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Datafile block
Almost all programs in the PHASE
package require a DATAFILE block to
parse analysed sequences. As stated previously, the DATAFILE block
begins with the tag {DATAFILE} alone on a line and ends with
the tag {DATAFILE} alone on a line.
The DATAFILE block contains some necessary information which is not
included in the data file itself (see the input file section for the format of this file); it contains the following
control lines:
-
Data file: the location of the molecular sequences file to be used.
Data file = data/sequences.dna
-
Interleaved data file: a yes/no option that specifies
whether the molecular data is interleaved.
Interleaved data file = yes
-
Outgroup: the label of the outgroup sequence. The inference techniques
used in PHASE
produce unrooted phylogenies and using an outgroup in
your study is not required. However PHASE
requires this parameter to produce
a unique newick representation
for unrooted trees.
Outgroup = Mole
-
Heterogeneous data models: is a yes/no parameter
which specifies whether the data file contains a class section. The default value is no and
the class section of your data file will be ignored if you forget this field.
Heterogeneous data models = yes
Next: Model block
Up: Control files
Previous: Structure of the control
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Gowri-Shankar Vivek
2003-04-24