# HG changeset patch # User dcorreia # Date 1458744936 14400 # Node ID 4c4532e366b328dce275643c864e19161f85f197 # Parent 9e083ac98a6d53ee11ea240c2e13e160aa14ad2f Uploaded diff -r 9e083ac98a6d -r 4c4532e366b3 phyml.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phyml.xml Wed Mar 23 10:55:36 2016 -0400 @@ -0,0 +1,314 @@ + + Phylogeny software based on the maximum-likelihood + + phyml + + + + + + + + + ${output_stdout}; + grep 'failed' ${output_stdout} >&2; + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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, --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, 00000 corresponds to F81, 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* 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 frequency + - *"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 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, --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, --nclasses nb_subst_cat + nb_subst_cat : number of relative substitution rate categories. Default : nb_subst_cat=4. + Must be a positive integer. + + -a, --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, --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, --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. + + - *tlr* : tree topology (t), branch length (l) and rate parameters (r) are optimised. + - *tl* : tree topology and branch length are optimised. + - *r* : branch length and rate parameters are optimised. + - *l* : branch length are optimised. + - *r* : rate parameters are optimised. + - *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 integer + Number of initial random trees to be used. + It is only valid if SPR searches are to be performed. + --r_seed integer + Number of the seed used to initiate the random number generator. + --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. + ]]> + + + 10.1093/sysbio/syq010 + +