Author: tille Date: 2011-02-14 16:23:16 +0000 (Mon, 14 Feb 2011) New Revision: 5979
Added: trunk/packages/phyml/trunk/debian/manpages trunk/packages/phyml/trunk/debian/phyml.1 Modified: trunk/packages/phyml/trunk/debian/changelog Log: Uploaded new upstream including newly written manpage Modified: trunk/packages/phyml/trunk/debian/changelog =================================================================== --- trunk/packages/phyml/trunk/debian/changelog 2011-02-14 15:43:16 UTC (rev 5978) +++ trunk/packages/phyml/trunk/debian/changelog 2011-02-14 16:23:16 UTC (rev 5979) @@ -1,9 +1,10 @@ -phyml (2:20100720-1) UNRELEASED; urgency=low +phyml (2:20100720-1) unstable; urgency=low * New upstream version * Fixed watch file * Standard-Version: 3.9.1 (no changes needed) * Source format 3.0 (quilt) + * Wrote man page -- Andreas Tille <[email protected]> Mon, 14 Feb 2011 15:04:52 +0100 Added: trunk/packages/phyml/trunk/debian/manpages =================================================================== --- trunk/packages/phyml/trunk/debian/manpages (rev 0) +++ trunk/packages/phyml/trunk/debian/manpages 2011-02-14 16:23:16 UTC (rev 5979) @@ -0,0 +1 @@ +debian/*.1 Added: trunk/packages/phyml/trunk/debian/phyml.1 =================================================================== --- trunk/packages/phyml/trunk/debian/phyml.1 (rev 0) +++ trunk/packages/phyml/trunk/debian/phyml.1 2011-02-14 16:23:16 UTC (rev 5979) @@ -0,0 +1,247 @@ +.TH PhyML "1" "3.0" "phyml " "User Commands" +.SH NAME +phyml \- Phylogenetic estimation using Maximum Likelihood +.SH SYNOPSIS: +.PP +phyml [command args] + +.IP +All the options below are optional (except '\-i' if you want to use the command\-line interface). +.PP + +Command options: + +.HP +\fB-i\fR (or \fB\-\-input\fR) \fIseq_file_name\fR +.IP +\fIseq_file_name\fR is the name of the nucleotide or amino\-acid sequence file in PHYLIP format. +.PP + +.HP +\fB\-d\fR (or \fB\-\-datatype\fR) \fIdata_type\fR +.IP +\fIdata_type\fR is 'nt' for nucleotide (default), 'aa' for amino\-acid sequences, or 'generic', +(use NEXUS file format and the 'symbols' parameter here). +.PP + +.HP +\fB\-q\fR (or \fB\-\-sequential\fR) +.IP +Changes interleaved format (default) to sequential format. +.PP + +.HP +\fB\-n\fR (or \fB\-\-multiple\fR) \fInb_data_sets\fR +.IP +\fInb_data_sets\fR is an integer corresponding to the number of data sets to analyse. +.PP + +.HP +\fB\-p\fR (or \fB\-\-pars\fR) +.OP +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. + +.HP +\fB\-b\fR (or \fB\-\-bootstrap\fR) \fIint\fR +.IP +\fIint > 0:\fR int is the number of bootstrap replicates. +.IP +\fIint = 0:\fR neither approximate likelihood ratio test nor bootstrap values are computed. +.IP +\fIint = \-1\fR: approximate likelihood ratio test returning aLRT statistics. +.IP +\fIint = \-2\fR: approximate likelihood ratio test returning Chi2\-based parametric branch supports. +.IP +\fIint = \-4\fR: (default) SH\-like branch supports alone. + +.HP +\fB\-m\fR (or \fB\-\-model\fR) \fImodel\fR +.IP +model : substitution model name. +\- \fINucleotide\fR\-based models : \fIHKY85\fR (default) | \fIJC69\fR | \fIK80\fR | \fIF81\fR | \fIF84\fR | \fITN93\fR | \fIGTR\fR | \fIcustom\fR +(for the custom option, a string of six digits identifies the model. For instance, 000000) +.IP +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. +.IP +\- \fIAmino\-acid\fR based models : \fILG\fR (default) | \fIWAG\fR | \fIJTT\fR | \fIMtREV\fR | \fIDayhoff\fR | \fIDCMut\fR | \fIRtREV\fR | \fICpREV\fR | \fIVT\fR +\fIBlosum62\fR | \fIMtMam\fR | \fIMtArt\fR | \fIHIVw\fR | +\fIHIVb\fR | \fIcustom\fR + +.HP +\fB\-\-aa_rate_file\fR \fIfilename\fR +.IP +\fIfilename\fR 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. +.PP + +.HP +\fB\-f\fR \fIe\fR, \fIm\fR, or \fIfA,fC,fG,fT\fR +.IP +\fIe\fR : the character frequencies are determined as follows : +.IP +\- Nucleotide sequences: (Empirical) the equilibrium base frequencies are estimated by counting +the occurence of the different bases in the alignment. +.IP +\- Amino\-acid sequences: (Empirical) the equilibrium amino\-acid frequencies are estimated by counting +the occurence of the different amino\-acids in the alignment. +.IP +\fIm\fR : the character frequencies are determined as follows : +.IP +\- Nucleotide sequences: (ML) the equilibrium base frequencies are estimated using maximum likelihood +.IP +\- Amino\-acid sequences: (Model) the equilibrium amino\-acid frequencies are estimated using +the frequencies defined by the substitution model. +.IP +\fI"fA,fC,fG,fT"\fR : 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!) + +.HP +\fB\-t\fR (or \fB\-\-ts\fR/tv) \fIts/tv_ratio\fR +.IP +\fIts/tv_ratio\fR : transition/transversion ratio. DNA sequences only. +Can be a fixed positive value (ex:4.0) or e to get the maximum likelihood estimate. + +.HP +\fB\-v\fR (or \fB\-\-pinv\fR) \fIprop_invar\fR +.IP +\fIprop_invar\fR: proportion of invariable sites. +Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate. + +.HP +\fB\-c\fR (or \fB\-\-nclasses\fR) \fInb_subst_cat\fR +.IP +\fInb_subst_cat\fR : number of relative substitution rate categories. Default: \fInb_subst_cat=4\fR. +Must be a positive integer. + +.HP +\fB\-a\fR (or \fB\-\-alpha\fR) \fIgamma\fR +.IP +\fIgamma\fR : distribution of the gamma distribution shape parameter. +Can be a fixed positive value or \fIe\fR to get the maximum likelihood estimate. + +.HP +\fB\-s\fR (or \fB\-\-search\fR) \fImove\fR +.IP +Tree topoLOGy search operation option. +Can be either \fINNI\fR (default, fast) or \fISPR\fR (a bit slower than NNI) or \fIBEST\fR (best of NNI and SPR search). + +.HP +\fB\-u\fR (or \fB\-\-inputtree\fR) \fIuser_tree_file\fR +.IP +\fIuser_tree_file\fR : starting tree filename. The tree must be in Newick format. + +.HP +\fB\-o\fR \fIparams\fR +.IP +This option focuses on specific parameter optimisation. +.IP +\fIparams\fR=tlr : tree topoLOGy (t), branch length (l) and rate parameters (r) are optimised. +.IP +\fIparams\fR=tl : tree topoLOGy and branch length are optimised. +.IP +\fIparams\fR=lr : branch length and rate parameters are optimised. +.IP +\fIparams\fR=l : branch length are optimised. +.IP +\fIparams\fR=r : rate parameters are optimised. +.IP +\fIparams\fR=n : no parameter is optimised. + +.HP +\fB\-\-rand_start\fR +.IP +This option sets the initial tree to random. It is only valid if SPR searches are to be performed. + +.HP +\fB\-\-n_rand_starts\fR \fInum\fR +.IP +\fInum\fR is the number of initial random trees to be used. +It is only valid if SPR searches are to be performed. + +.HP +\fB\-\-r_seed\fR \fInum\fR +.IP +\fInum\fR is the seed used to initiate the random number generator. +Must be an integer. + +.HP +\fB\-\-print_site_lnl\fR +.IP +Print the likelihood for each site in file *_phyml_lk.txt. +.PP + +.HP +\fB\-\-print_trace\fR +.IP +Print each phyLOGeny explored during the tree search process +in file *_phyml_trace.txt. + +.HP +\fB\-\-run_id\fR \fIID_string\fR +.IP +Append the string \fIID_string\fR at the end of each PhyML output file. +This option may be useful when running simulations involving PhyML. +.PP + +.HP +\fB\-\-quiet\fR +.IP +No interactive question (for running in batch mode) and quiet output. +.PP + +.HP +\fB\-\-no_memory_check\fR +.IP +No interactive question for memory usage (for running in batch mode). Normal ouput otherwise. +.PP + +.HP +\fB\-\-alias_subpatt\fR +.IP +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. +.PP + +.HP +\fB\-\-boot_progress_display\fR \fInum\fR (default=20) +.IP +\fInum\fR is the frequency at which the bootstrap progress bar will be updated. +Must be an integer. + +.SH PHYLIP\-LIKE INTERFACE +.PP +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. + +.SH EXAMPLES +.PP +DNA interleaved sequence file, default parameters : +.IP +\fBphyml \-i seqs1\fR +.PP +AA interleaved sequence file, default parameters : +.IP +\fBphyml \-i seqs2 \-d aa\fR +.TP +AA sequential sequence file, with customization : +.IP +\fBphyml \-i seqs3 \-q \-d aa \-m JTT \-c 4 \-a e\fR + +.SH "SEE ALSO" +.PP +A simple, fast, and accurate algorithm to estimate large phyLOGenies by maximum likelihood +.PP +Stephane Guindon and Olivier Gascuel, +Systematic BioLOGy 52(5):696\-704, 2003. +.PP +Please cite this paper if you use this software in your publications. + +.SH AUTHOR +\fBPhyML\fP was written by Stephane Guindon and Olivier Gascuel +and others +.PP +This manual page was written by Andreas Tille <[email protected]>, +for the Debian project (but may be used by others). _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
