Bio::Tools::Run::Phylo::PAML::Baseml - Wrapper aroud the PAML program baseml use Bio::Tools::Run::Phylo::PAML::Baseml; use Bio::AlignIO; my $alignio = new Bio::AlignIO(-format => 'phylip', -file => 't/data/gf-s85.phylip'); my $aln = $alignio->next_aln; my $bml = new Bio::Tools::Run::Phylo::PAML::Baseml(); $bml->alignment($aln); my ($rc,$parser) = $bml->run(); while( my $result = $parser->next_result ) { my @otus = $result->get_seqs(); my $MLmatrix = $result->get_MLmatrix(); # 0 and 1 correspond to the 1st and 2nd entry in the @otus array } This is a wrapper around the baseml program of PAML (Phylogenetic Analysis by Maximum Likelihood) package of Ziheng Yang. See http://abacus.gene.ucl.ac.uk/software/paml.html for more information. This module will generate a proper baseml.ctl file and will run the program in a separate temporary directory to avoid creating temp files all over the place and will cleanup after itself.. The values you can feed to the configuration file are documented here. 'noisy' => [ 0..3,9], 'verbose' => [ 0,1,2], # 0:concise, 1:detailed, 2:too much 'runmode' => [-2,0..5], # for runmode # -2 pairwise # 0: use the provided tree structure(s) in treefile # 1,2: mean heuristic search by star-decomposition alg # 2: starts from star tree while 1 reads a multifurcating # tree from treefile and ties to estimate the best # bifurcating tree # 3: stepwise addition # 4: NNI perturbation with the starting tree # Tree search DOES NOT WORK WELL so estimate a tree # using other programs first 'model' => '0', # for model # 0: JC69 (uncorrected) # 1: K80 (transitions/transversion weighted differently) # 2: F81 # 3: F84 # 4: HKY85 # 5: T92 (Tamura 92) # 6: TN93 (Tajima-Nei) correct for multiple substitutions # 7: REV (aka GTR) # 8: UNREST # 9: REVu #10: UNRESTu # See Yang 1994 JME 39:105-111 # model 8 special case of the REV model # model 9 is special case of unrestricted model # can also supply special rate parameters # so for example (from pamlDOC.pdf # $model = '8 [2 (CT) (AG)]'; # TN93 # $model = '8 [2 (TA AT TG CA CG) (AG)]'; # TN93 # $model = '9 [1 (TC CT AG GA)]; # K80 # $model = '9 [0]'; # JC69 # $model = '9 [11 (TA) (TG) (CT) (CA) (CG) (AT) (AC) (AG) (GT) (GC) (GA)], 'outfile' => 'mlb', 'fix_kappa'=> [0,1], # 0:estimate kappa, 1:fix kappa 'kappa' => '2.5', # initial or fixed kappa 'fix_alpha'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'alpha' => '0', # initial of fixed alpha # 0: infinity (constant rate) 'Malpha' => [0,1], # different alphas for genes 'fix_rho'=> [1,0], # 0: estimate gamma shape param # 1: fix it at alpha 'rho' => '0', # initial of fixed alpha # 0: infinity (constant rate) 'ncatG' => '5', # number of categories in the dD,AdG, or nparkK models of rates 'nparK' => [0..4], # rate-class models # 1:rk 2:rk&fK # 3:rK&MK(1/K) 4:rK&MK 'nhomo' => [0..4], # 0 & 1: homogeneous, # 2: kappa for brances # 3:N1 4:N2 'getSE' => [0,1], 'RateAncestor' => [1,0,2], # rates (alpha > 0) or # ancestral states 'cleandata' => [1,0], # remove sites with # ambiguity data (1:yes or 0:no) 'fix_blength' => [-1,0,1,2], # 0: ignore, -1: random, # 1: initial, 2: fixed # 'icode' => [ 0..10], # (with RateAncestor=1. #try "GC" in data,model=4,Mgene=4) 'ndata' => [5,1..10], 'clock' => [0..3], # 0: no clock, 1: clock, 2: local clock, 3: CombinedAnalysis 'Small_Diff' => '1e-6', #underflow issues?

Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists

Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web: http://bugzilla.bioperl.org/ Email jason-at-bioperl.org Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

Default Values

program_name
Title : program_name Usage : $obj->program_name() Function: holds the program name Returns: string Args : None

program_dir
Title : program_dir Usage : ->program_dir() Function: returns the program directory, obtiained from ENV variable. Returns: string Args :

new
Title : new Usage : my $obj = new Bio::Tools::Run::Phylo::PAML::Yn00(); Function: Builds a new Bio::Tools::Run::Phylo::PAML::Yn00 object Returns : Bio::Tools::Run::Phylo::PAML::Yn00 Args : -alignment => the L<Bio::Align::AlignI> object -save_tempfiles => boolean to save the generated tempfiles and NOT cleanup after onesself (default FALSE)

run
Title : run Usage : $yn->run(); Function: run the yn00 analysis using the default or updated parameters the alignment parameter must have been set Returns : 3 values, $rc = 1 for success, 0 for errors hash reference of the Yang calculated Ka/Ks values this is a set of pairwise observations keyed as sequencenameA->sequencenameB->datatype hash reference same as the previous one except it for the Nei and Gojobori calculated Ka,Ks,omega values Args : none

error_string
Title : error_string Usage : $obj->error_string($newval) Function: Where the output from the last analysus run is stored. Returns : value of error_string Args : newvalue (optional)

alignment
Title : alignment Usage : $codeml->align($aln); Function: Get/Set the L<Bio::Align::AlignI> object Returns : L<Bio::Align::AlignI> object Args : [optional] L<Bio::Align::AlignI> Comment : We could potentially add support for running directly on a file but we shall keep it simple See also: L<Bio::SimpleAlign>

get_parameters
Title : get_parameters Usage : my %params = $self->get_parameters(); Function: returns the list of parameters as a hash Returns : associative array keyed on parameter names Args : none

set_parameter
Title : set_parameter Usage : $codeml->set_parameter($param,$val); Function: Sets a codeml parameter, will be validated against the valid values as set in the %VALIDVALUES class variable. The checks can be ignored if on turns of param checks like this: $codeml->no_param_checks(1) Returns : boolean if set was success, if verbose is set to -1 then no warning will be reported Args : $paramname => name of the parameter $value => value to set the parameter to See also: L<no_param_checks()>

set_default_parameters
Title : set_default_parameters Usage : $codeml->set_default_parameters(0); Function: (Re)set the default parameters from the defaults (the first value in each array in the %VALIDVALUES class variable) Returns : none Args : boolean: keep existing parameter values

no_param_checks
Title : no_param_checks Usage : $obj->no_param_checks($newval) Function: Boolean flag as to whether or not we should trust the sanity checks for parameter values Returns : value of no_param_checks Args : newvalue (optional)

save_tempfiles
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)

outfile_name
Title : outfile_name Usage : my $outfile = $codeml->outfile_name(); Function: Get/Set the name of the output file for this run (if you wanted to do something special) Returns : string Args : [optional] string to set value to

tempdir
Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none

cleanup
Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory after a PAML run Returns : none Args : none

io
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none