You can also use
nhPhyml directly from the command line using :
./nhPhyml
-sequences=SequenceFile -tree=TreeFile -format=i -positions=123 -tstv=e
-rates=8 -alpha=e -topology=e -outseqs=y -eqfreq=lim -numeqfreq=5
-treefile=Treefile
Where
:
SequenceFile is the
sequence file in phylip format,
TreeFile is the
starting tree file in bracketted (newick) format
-format=i helps
specifying phylip interleaved format (can also be s for phylip sequential
format),
-positions=123
means that the user wants to use all the positions in the codons (could also be 1, 12,
13, 2, 23, or 3)
-tstv=e is to
tell the program that the transition/transversion rate needs to be
evaluated (put a value otherwise),
-rates=8 is the
number of rate categories for the discretized gamma distribution,
-alpha=e means
that the gamma distribution parameter alpha is to be evaluated (put a
value otherwise),
-topology=e
means that we want to optimize the topology and the branch lengthes ; putting k for keep
would only optimize branch length while keeping the topology,
-eqfreq=lim
means we want to use the nhPhyML-Discrete version of nhPhyML, which
means that each branch has the "choice" between a limited set of G+C
equilibrium frequencies.
In the default
version, specified by -eqfreq=unlim, the G+C equilibrium frequency is
optimized for each branch. This results in some convergence problems
(the true topology is found less often than with -eqfreq=lim).
-numeqfreq=5 :
in case you use a limited set of equilibrium frequencies (-eqfreq=lim),
you need to specify the number of equilibrium frequencies you want to
use. This number is important : too small, and the process of evolution
might not be modelled correctly. Too big, and the tree space
exploration gets unefficient. Please refer to the article for more
details. Recent addition (20/07/2012): Now you can specify upper and lower values for the limited set of equilibrium frequencies. Use options -eqfreqlow=0.2 -eqfrequpp=0.8 for instance.
Only the sequence file and the
tree file are mandatory. Default values for the other parameters
are :
-format=i
-positions=123 -tstv=e -rates=1 -topology=e -outseqs=n -eqfreq=unlim
When there is
only one rate of evolution, no alpha is used.