== INSTALATION ==

On UNIX-like operating system (i.e., Mac OS X and Linux), type the following commands in a terminal window:

aclocal; autoheader; autoconf -f; automake -f --add-missing; ./configure; make clean; make;

In order to install the program 'coltree' that will help you visualise the results of a fitmodel analysis, type the following commands:

aclocal; autoheader; autoconf -f; automake -f --add-missing; ./configure --enable-coltree; make clean; make;

== DESCRIPTION ==

'Fitmodel' estimates the parameters of various codon-based models of substitution, including those described in Guindon, Rodrigo, Dyer and Huelsenbeck (2004). These models are especially useful as they accommodate site-specific switches between selection regimes without a priori knowledge of the positions in the tree where changes of selection regimes occurred.

The program will ask for two input files: a tree file and a sequence file. The tree should be unrooted and in NEWICK format. fitmodel will crash if you feed him with a rooted tree. The sequences should be in PHYLIP interleaved or sequential format. If you are planning to use codon-based models, the sequence length should be a multiple of 3. The program provides four types of codon models: M1, M2, M2a, and M3 (see PAML manual). Moreover, M2, M2a and M3 can be combined with 'switching' models (option 'M'). Two switching models are implemented: S1 and S2. S1 constraints the rates of changes between dN/dS values to be uniform (e.g., the rates of changes between negative and positive selection is constrained to be the same as the rate of change between neutrality and positive selection) while S2 allows for differents rates of change between the different classes of dN/dS values.

If you are using a 'switching' model, 'fitmodel' will output file with the following names: your_sequence_file_trees_w1, your_sequence_file_trees_w2, your_sequence_file_trees_w3 and your_sequence_file_trees_wbest. The w1, w2 and w3 files give the estimated tree with probabilities of w1, w2, and w3 (three maximum likelihood dN/dS ratio estimates) calculated on each edge of the tree and for each site. Hence, the first tree in one of these files reports the probabilities calculated at the first site of the alignment. Instead of probabilities, the wbest file allows you to identify which of the tree dN/dS is the most probable on any give edge, at any given site. A branch with label 0.0 means that w1 is the most probable class, 0.5 indicates the w2 is the most probable and 1.0 means that w3 has the highest posterior probability.

Processing those results manually can be very tedious. The program 'coltree' reads 'fitmodel' output file and generates a postscript file which displays the phylogeny at each codon site with different colors on edges depending on the posterior probabilities estimated on each branch, at each site (see file p1.pdf). This is very useful to detect site specific changes of selection regimes. To compile 'coltree' on UNIX-like systems, simply type the following commands in a terminal window:

This will generate the binary for 'coltree'. 'coltree' is a command-line program that takes as first argument 'fitmodel' output tree file. The second argument is the name of the postscript file where the trees will be written.

== EXAMPLE ==

The directory example/ contains a sequence file (p1.nxs) and a tree file (p1.tree) that can be processed by fitmodel. The files p1.nxs_fitmodel_stats, p1.nxs_fitmodel_tree, p1.nxs_trees_w1, p1.nxs_trees_w2, p1.nxs_trees_w3 and p1.nxs_trees_wbest were generated by 'fitmodel' using the M2a+S1 model. The command line that was used in order to generate those files is the following one:

./fitmodel < param

where 'param' is a text file that contains the series of letters one have to enter in order to select the M2a+S1 model (and other options) through the PHYLIP-like interface.

The file 'tree.ps' is a postscript file that displays the posterior probability of w1 on each edge at each code site of the alignment. It was generated using the following command-line:

./coltree p1.nxs_trees_w1 tree.ps

====

Need more help? Contact me: stephane.guindon@lirmm.fr

BIBLIOGRAPHY

"Modeling the site-specific variation of selection patterns along lineages" Stephane Guindon, Allen G Rodrigo, Kelly A Dyer, John P Huelsenbeck Proceedings of the National Academy of Sciences of the United States of America 2004

"Modelling the variability of evolutionary processes" Olivier Gascuel, Stephane Guindon Reconstructing evolution. New mathematical and computational advances. Oxford University Press 2007