The present function has been tested with version 2.4 of PHYML; it
should also work with version 2.3, but it won't work with version 2.1. Under unix-like systems, it seems necessary to run R from csh or a
similar shell (sh might not work).
The user must take care to set correctly the three different paths
involved here: the path to PHYML's binary, the path to the sequence
file, and the path to R's working directory. The function should work
if all three paths are different. Obviously, there should be no problem
if they are all the same.
If the usual output files of PHYML already exist, they are not
deleted and PHYML's results are appended.
The following syntax is used for the models:
"X[Y][Z]00[+I][+G]"
where "X" is the first letter of the author of the model, "Y" and "Z"
are possibly other co-authors of the model, "00" is the year of the
publication of the model, and "+I" and "+G" indicates whether the
presence of invariant sites and/or a gamma distribution of
substitution rates have been specified. Thus, Kimura's model is
denoted "K80" and not "K2P". The exception to this rule is the general
time-reversible model which is simple denoted "GTR" model.
The seven substitution models used are: "JC69", "K80", "F81", "F84",
"HKY85", "TN93", and "GTR". These models are then altered by adding
the "+I" and/or "+G", resulting thus in four variants for each of them
(e.g., "JC69", "JC69+I", "JC69+G", "JC69+I+G"). Some of these models
are described in the help page of dist.dna
.
When a gamma distribution of substitution rates is specified, four
categories are used (which is PHYML's default behaviour), and the
``alpha'' parameter is estimated from the data.
For the models with a different substition rate for transitions and
transversions, these rates are left free and estimated from the data
(and not constrained with a ratio of 4 as in PHYML's default).