Phylogenetic tree

NAME
- PhyML 20120412 -

''A simple, fast, and accurate algorithm to estimate
large phylogenies by maximum likelihood''

Stephane Guindon and Olivier Gascuel,
Systematic Biology 52(5):696-704, 2003.

Please cite this paper if you use this software in your publications.

SYNOPSIS:

phyml [command args]

All the options below are optional (except '-i' if you want to use the command-line interface).


Command options:

-i (or --input) seq_file_name
seq_file_name is the name of the nucleotide or amino-acid sequence file in PHYLIP format.


-d (or --datatype) data_type
data_type is 'nt' for nucleotide (default), 'aa' for amino-acid sequences, or 'generic',
(use NEXUS file format and the 'symbols' parameter here).


-q (or --sequential)
Changes interleaved format (default) to sequential format.


-n (or --multiple) nb_data_sets
nb_data_sets is an integer corresponding to the number of data sets to analyse.


-p (or --pars)
Use a minimum parsimony starting tree. This option is taken into account when the '-u' option
is absent and when tree topology modifications are to be done.


-b (or --bootstrap) int
int > 0: int is the number of bootstrap replicates.
int = 0: neither approximate likelihood ratio test nor bootstrap values are computed.
int = -1: approximate likelihood ratio test returning aLRT statistics.
int = -2: approximate likelihood ratio test returning Chi2-based parametric branch supports.
int = -4: (default) SH-like branch supports alone.
int = -5: approximate Bayes branch supports.


-m (or --model) model
model : substitution model name.
- Nucleotide-based models : HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR | custom (*)
(*) : for the custom option, a string of six digits identifies the model. For instance, 000000
corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform).
012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR.

- Amino-acid based models : LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV | CpREV | VT
Blosum62 | MtMam | MtArt | HIVw | HIVb | custom


--aa_rate_file filename
filename is the name of the file that provides the amino acid substitution rate matrix in PAML format.
It is compulsory to use this option when analysing amino acid sequences with the `custom' model.


-f e, m, or fA,fC,fG,fT
e : the character frequencies are determined as follows :
- Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting
the occurence of the different bases in the alignment.
- Amino-acid sequences: (Empirical) the equilibrium amino-acid frequencies are estimated by counting
the occurence of the different amino-acids in the alignment.

m : the character frequencies are determined as follows :
- Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood
- Amino-acid sequences: (Model) the equilibrium amino-acid frequencies are estimated using
the frequencies defined by the substitution model.

"fA,fC,fG,fT" : only valid for nucleotide-based models. fA, fC, fG and fT are floating numbers that
correspond to the frequencies of A, C, G and T respectively (WARNING: do not use any blank space between
your values of nucleotide frequencies, only commas!)


-t (or --ts/tv) ts/tv_ratio
ts/tv_ratio : transition/transversion ratio. DNA sequences only.
Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate.


-v (or --pinv) prop_invar
prop_invar : proportion of invariable sites.
Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate.


-c (or --nclasses) nb_subst_cat
nb_subst_cat : number of relative substitution rate categories. Default : nb_subst_cat=4.
Must be a positive integer.


-a (or --alpha) gamma
gamma : distribution of the gamma distribution shape parameter.
Can be a fixed positive value or e to get the maximum likelihood estimate.


-s (or --search) move
Tree topology search operation option.
Can be either NNI (default, fast) or SPR (a bit slower than NNI) or BEST (best of NNI and SPR search).


-u (or --inputtree) user_tree_file
user_tree_file : starting tree filename. The tree must be in Newick format.


-o params
This option focuses on specific parameter optimisation.
params=tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
params=tl : tree topology and branch length are optimised.
params=lr : branch length and rate parameters are optimised.
params=l : branch length are optimised.
params=r : rate parameters are optimised.
params=n : no parameter is optimised.


--rand_start
This option sets the initial tree to random.
It is only valid if SPR searches are to be performed.


--n_rand_starts num
num is the number of initial random trees to be used.
It is only valid if SPR searches are to be performed.


--r_seed num
num is the seed used to initiate the random number generator.
Must be an integer.


--print_site_lnl
Print the likelihood for each site in file *_phyml_lk.txt.


--print_trace
Print each phylogeny explored during the tree search process
in file *_phyml_trace.txt.


--run_id ID_string
Append the string ID_string at the end of each PhyML output file.
This option may be useful when running simulations involving PhyML.


--quiet
No interactive question (for running in batch mode) and quiet output.


--no_memory_check
No interactive question for memory usage (for running in batch mode). Normal ouput otherwise.


--alias_subpatt
Site aliasing is generalized at the subtree level. Sometimes lead to faster calculations.
See Kosakovsky Pond SL, Muse SV, Sytematic Biology (2004) for an example.


--boot_progress_display num (default=20)
num is the frequency at which the bootstrap progress bar will be updated.
Must be an integer.

PHYLIP-LIKE INTERFACE

You can also use PhyML with no argument, in this case change the value of
a parameter by typing its corresponding character as shown on screen.

EXAMPLES

DNA interleaved sequence file, default parameters : ./phyml -i seqs1
AA interleaved sequence file, default parameters : ./phyml -i seqs2 -d aa
AA sequential sequence file, with customization : ./phyml -i seqs3 -q -d aa -m JTT -c 4 -a e
sergey@serfer:~/server/programs$ ./phyml3 --help

NAME
- PhyML 20120412 -

''A simple, fast, and accurate algorithm to estimate
large phylogenies by maximum likelihood''

Stephane Guindon and Olivier Gascuel,
Systematic Biology 52(5):696-704, 2003.

Please cite this paper if you use this software in your publications.

SYNOPSIS:

phyml [command args]

All the options below are optional (except '-i' if you want to use the command-line interface).


Command options:

-i (or --input) seq_file_name
seq_file_name is the name of the nucleotide or amino-acid sequence file in PHYLIP format.


-d (or --datatype) data_type
data_type is 'nt' for nucleotide (default), 'aa' for amino-acid sequences, or 'generic',
(use NEXUS file format and the 'symbols' parameter here).


-q (or --sequential)
Changes interleaved format (default) to sequential format.


-n (or --multiple) nb_data_sets
nb_data_sets is an integer corresponding to the number of data sets to analyse.


-p (or --pars)
Use a minimum parsimony starting tree. This option is taken into account when the '-u' option
is absent and when tree topology modifications are to be done.


-b (or --bootstrap) int
int > 0: int is the number of bootstrap replicates.
int = 0: neither approximate likelihood ratio test nor bootstrap values are computed.
int = -1: approximate likelihood ratio test returning aLRT statistics.
int = -2: approximate likelihood ratio test returning Chi2-based parametric branch supports.
int = -4: (default) SH-like branch supports alone.
int = -5: approximate Bayes branch supports.


-m (or --model) model
model : substitution model name.
- Nucleotide-based models : HKY85 (default) | JC69 | K80 | F81 | F84 | TN93 | GTR | custom (*)
(*) : for the custom option, a string of six digits identifies the model. For instance, 000000
corresponds to F81 (or JC69 provided the distribution of nucleotide frequencies is uniform).
012345 corresponds to GTR. This option can be used for encoding any model that is a nested within GTR.

- Amino-acid based models : LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV | CpREV | VT
Blosum62 | MtMam | MtArt | HIVw | HIVb | custom


--aa_rate_file filename
filename is the name of the file that provides the amino acid substitution rate matrix in PAML format.
It is compulsory to use this option when analysing amino acid sequences with the `custom' model.


-f e, m, or fA,fC,fG,fT
e : the character frequencies are determined as follows :
- Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting
the occurence of the different bases in the alignment.
- Amino-acid sequences: (Empirical) the equilibrium amino-acid frequencies are estimated by counting
the occurence of the different amino-acids in the alignment.

m : the character frequencies are determined as follows :
- Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood
- Amino-acid sequences: (Model) the equilibrium amino-acid frequencies are estimated using
the frequencies defined by the substitution model.

"fA,fC,fG,fT" : only valid for nucleotide-based models. fA, fC, fG and fT are floating numbers that
correspond to the frequencies of A, C, G and T respectively (WARNING: do not use any blank space between
your values of nucleotide frequencies, only commas!)


-t (or --ts/tv) ts/tv_ratio
ts/tv_ratio : transition/transversion ratio. DNA sequences only.
Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate.


-v (or --pinv) prop_invar
prop_invar : proportion of invariable sites.
Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate.


-c (or --nclasses) nb_subst_cat
nb_subst_cat : number of relative substitution rate categories. Default : nb_subst_cat=4.
Must be a positive integer.


-a (or --alpha) gamma
gamma : distribution of the gamma distribution shape parameter.
Can be a fixed positive value or e to get the maximum likelihood estimate.


-s (or --search) move
Tree topology search operation option.
Can be either NNI (default, fast) or SPR (a bit slower than NNI) or BEST (best of NNI and SPR search).


-u (or --inputtree) user_tree_file
user_tree_file : starting tree filename. The tree must be in Newick format.


-o params
This option focuses on specific parameter optimisation.
params=tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
params=tl : tree topology and branch length are optimised.
params=lr : branch length and rate parameters are optimised.
params=l : branch length are optimised.
params=r : rate parameters are optimised.
params=n : no parameter is optimised.


--rand_start
This option sets the initial tree to random.
It is only valid if SPR searches are to be performed.


--n_rand_starts num
num is the number of initial random trees to be used.
It is only valid if SPR searches are to be performed.


--r_seed num
num is the seed used to initiate the random number generator.
Must be an integer.


--print_site_lnl
Print the likelihood for each site in file *_phyml_lk.txt.


--print_trace
Print each phylogeny explored during the tree search process
in file *_phyml_trace.txt.


--run_id ID_string
Append the string ID_string at the end of each PhyML output file.
This option may be useful when running simulations involving PhyML.


--quiet
No interactive question (for running in batch mode) and quiet output.


--no_memory_check
No interactive question for memory usage (for running in batch mode). Normal ouput otherwise.


--alias_subpatt
Site aliasing is generalized at the subtree level. Sometimes lead to faster calculations.
See Kosakovsky Pond SL, Muse SV, Sytematic Biology (2004) for an example.


--boot_progress_display num (default=20)
num is the frequency at which the bootstrap progress bar will be updated.
Must be an integer.

PHYLIP-LIKE INTERFACE

You can also use PhyML with no argument, in this case change the value of
a parameter by typing its corresponding character as shown on screen.

EXAMPLES

DNA interleaved sequence file, default parameters : ./phyml -i seqs1
AA interleaved sequence file, default parameters : ./phyml -i seqs2 -d aa
AA sequential sequence file, with customization : ./phyml -i seqs3 -q -d aa -m JTT -c 4 -a e

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