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1PhyML-20130708
2
3DESCRIPTION
4        ''A simple, fast, and accurate algorithm to estimate
5        large phylogenies by maximum likelihood''
6
7        Stephane Guindon and Olivier Gascuel,
8        Systematic Biology 52(5):696-704, 2003.
9
10        Please cite this paper if you use this software in your publications.
11       
12PARAMETERS
13        -i (or --input) seq_file_name
14            seq_file_name is the name of the nucleotide or amino-acid sequence file in PHYLIP format.
15
16
17        -d (or --datatype) data_type
18            data_type is 'nt' for nucleotide (default), 'aa' for amino-acid sequences, or 'generic',
19            (use NEXUS file format and the 'symbols' parameter here).
20
21
22        -q (or --sequential)
23            Changes interleaved format (default) to sequential format.
24
25
26        -n (or --multiple) nb_data_sets
27            nb_data_sets is an integer corresponding to the number of data sets to analyse.
28
29
30        -p (or --pars)
31            Use a minimum parsimony starting tree. This option is taken into account when the '-u' option
32            is absent and when tree topology modifications are to be done.
33
34
35        -b (or --bootstrap) int
36            int >  0: int is the number of bootstrap replicates.
37            int =  0: neither approximate likelihood ratio test nor bootstrap values are computed.
38            int = -1: approximate likelihood ratio test returning aLRT statistics.
39            int = -2: approximate likelihood ratio test returning Chi2-based parametric branch supports.
40            int = -4: SH-like branch supports alone.
41            int = -5: (default) approximate Bayes branch supports.
42
43
44        -m (or --model) model
45            model : substitution model name.
46            - Nucleotide-based models : HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR | custom (*)
47
48             (*) : for the custom option, a string of six digits identifies the model. For instance, 000000
49             corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform).
50             012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR.
51
52            - Amino-acid based models : LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV | CpREV | VT
53              Blosum62 | MtMam | MtArt | HIVw | HIVb | custom
54
55
56        --aa_rate_file filename
57            filename is the name of the file that provides the amino acid substitution rate matrix in PAML format.
58            It is compulsory to use this option when analysing amino acid sequences with the `custom' model.
59
60
61        -f e, m,  or  fA,fC,fG,fT
62
63            - e : the character frequencies are determined as follows :
64                - Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting
65                  the occurence of the different bases in the alignment.
66                - Amino-acid sequences: (Empirical) the equilibrium amino-acid frequencies are estimated by counting
67                  the occurence of the different amino-acids in the alignment.
68            - m : the character frequencies are determined as follows :
69                - Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood
70                - Amino-acid sequences: (Model) the equilibrium amino-acid frequencies are estimated using
71                  the frequencies defined by the substitution model.
72            - "fA,fC,fG,fT" : only valid for nucleotide-based models.
73
74                  fA, fC, fG and fT are floating numbers that correspond to the frequencies of A, C, G and T
75                  respectively (WARNING: do not use any blank space between your values of nucleotide frequencies, only commas!)
76
77
78        -t (or --ts/tv) ts/tv_ratio
79            ts/tv_ratio : transition/transversion ratio. DNA sequences only.
80            Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate.
81
82
83        -v (or --pinv) prop_invar
84            prop_invar : proportion of invariable sites.
85            Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate.
86
87
88        -c (or --nclasses) nb_subst_cat
89            nb_subst_cat : number of relative substitution rate categories. Default : nb_subst_cat=4.
90            Must be a positive integer.
91
92
93        -a (or --alpha) gamma
94            gamma : distribution of the gamma distribution shape parameter.
95            Can be a fixed positive value or e to get the maximum likelihood estimate.
96
97
98        -s (or --search) move
99            Tree topology search operation option.
100            Can be either NNI (default, fast) or SPR (a bit slower than NNI) or BEST (best of NNI and SPR search).
101
102
103        -u (or --inputtree) user_tree_file
104            user_tree_file : starting tree filename. The tree must be in Newick format.
105
106
107        -o params
108            This option focuses on specific parameter optimisation.
109            params=tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
110            params=tl  : tree topology and branch length are optimised.
111            params=lr  : branch length and rate parameters are optimised.
112            params=l   : branch length are optimised.
113            params=r   : rate parameters are optimised.
114            params=n   : no parameter is optimised.
115
116
117        --rand_start
118            This option sets the initial tree to random.
119            It is only valid if SPR searches are to be performed.
120
121
122        --n_rand_starts num
123            num is the number of initial random trees to be used.
124            It is only valid if SPR searches are to be performed.
125
126
127        --r_seed num
128            num is the seed used to initiate the random number generator.
129            Must be an integer.
130
131
132        --print_site_lnl
133            Print the likelihood for each site in file *_phyml_lk.txt.
134
135
136        --print_trace
137            Print each phylogeny explored during the tree search process
138            in file *_phyml_trace.txt.
139
140
141        --run_id ID_string
142            Append the string ID_string at the end of each PhyML output file.
143            This option may be useful when running simulations involving PhyML.
144
145
146        --quiet
147            No interactive question (for running in batch mode) and quiet output.
148
149
150        --no_memory_check
151            No interactive question for memory usage (for running in batch mode). Normal ouput otherwise.
152
153
154        --alias_subpatt
155            Site aliasing is generalized at the subtree level. Sometimes lead to faster calculations.
156            See Kosakovsky Pond SL, Muse SV, Sytematic Biology (2004) for an example.
157
158
159        --boot_progress_display num (default=20)
160            num is the frequency at which the bootstrap progress bar will be updated.
161            Must be an integer.
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