phyml_multi needs a sequence file in
phylip format.
Go to its
installation directory and type :
./phyml_multi
Then you face a
phylip-like (and PhyML-like) interface which asks for self-explanatory
information such as the number of rate categories for the gamma law,
whether or not the transition/transversion rate should be optimized...
You can also use
phyml_multi directly from the command line using :
./phyml_multi seqs1 0 i 2 0 HKY 4.0 e 1 1.0 BIONJ y n n 2
Where
:
seqs1 :
sequence file in phylip format,
0 | 1 : put 0 if working with nucleotide sequences, 1 for amino-acid sequences
i : helps
specifying phylip interleaved format (can also be s for phylip sequential
format),
2 : number of datasets to analyse (cannot be below 1!)
0 : number of bootstrap sets to generate
HKY : name of the model to be used (JC69 | K2P | F81 | HKY | F84 | TN93 for nucleotide sequences, JTT | MtREV | Dayhoff | WAG for amino-acid sequences)
4.0 : transition/transversion ration; putting "e" lets the program evaluate this ratio
e : proportion of invariable sites; putting "e" lets the program evaluate this proportion
1 : number of substitution rate categories
1.0 : shape parameter of the gamma distribution; putting "e" lets the program evaluate this parameter
BIONJ : technique used to build starting trees, or alternatively, file containing starting trees
y | n : should we optimize the tree topology
y | n : should we optimize branch lengths
y | n : should we use a Hidden Markov Model instead of the Mixture Model on trees
2 : Number of trees expected in the alignment
When there is
only one rate of evolution, no alpha is used.
Several files are
produced in the directory containing the "SequenceFile". The most important ones are as follow :
-
SequenceFile_phyml.lk possesses 2 or 3 lines : the first one displays the final
likelihood of the output trees, the second one (if the HMM option has been chosen) gives the value of the autocorrelation parameter, and the last line gives the time used for the computation.
-
SequenceFile_phyml_siteLks.txt contains a table showing site likelihoods and log-likelihoods for each tree. This file is then used as input for the python scripts that produce the segmentation.
-
SequenceFile_phyml_tree.txtX contains the tree number X