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https://github.com/nylander/pmraic

Parallel MrAIC
https://github.com/nylander/pmraic

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Parallel MrAIC

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README 

          
pMrAIC - Parallel MrAIC

======



NAME



    pmraic.pl



VERSION



    Documentation for pmraic.pl version 1.1



SYNOPSIS



    pmraic.pl [options] FILE



DESCRIPTION



    Script for running nucleotide substitutions using PHYML (Guindon &

    Gasquel, 2003) in parallel. It will report the best AIC, AICc, BIC

    model(s), along with the best ML tree under that/those models, and also

    the syntax for specifying the model(s) in MrBayes v.3 (Ronquist &

    Huelsenbeck, 2003).



OPTIONS



    Mandatory arguments to long options are mandatory for short options too



    -b, --bash=*number*

            Generate *number* of bash scripts for running PHYML. Can be

            manually distributed to several machines. Use *--summarize*

            later for collecting the output. Using this option will not

            start PHYML, but the analyses have to be started manually (using

            the scripts).



    -c, --cpu=*number*

            Number of "CPUs" to use. Default is to run as many as the number

            of available cores.



    -i, --infile=*infile*

            Excplicitly specify the *infile* to be used. The infile should

            have nt sequences and be readable by phyml.



    -mau, --maui

            Create submit files for the Maui cluster scheduler system. Use

            *--summarize* later for collecting the output.



    -models, --models=*arg1,arg2,...,argn*

            Specify a subset of the 56 models available to be run by PHYML.

            *arg1,arg2,...,argn* should be given as a comma-separated list.

            No spaces. Note that a MrBayes block will only be printed if the

            best model is among the 24 nt models available in MrBayes v.3.

            Valid model names are (first 24 are available in MrBayes):



                F81,F81G,F81I,F81IG,GTR,GTRG,

                GTRI,GTRIG,HKY85,HKY85G,HKY85I,HKY85IG,

                JC69,JC69G,JC69I,JC69IG,K2P,K2PG,

                K2PI,K2PIG,SYM,SYMG,SYMI,SYMIG



                K3P,K3PG,K3PI,K3PIG,K3PUF,K3PUFG,

                K3PUFI,K3PUFIG,TIM,TIMEF,TIMEFG,TIMEFI,

                TIMEFIG,TIMG,TIMI,TIMIG,TRN,TRNEF,

                TRNEFG,TRNEFI,TRNEFIG,TRNG,TRNI,TRNIG,

                TVM,TVMEF,TVMEFG,TVMEFI,TVMEFIG,TVMG,

                TVMI,TVMIG,



    -modelt, --modeltest

            Run all 56 models.



    -o, --optimize=*arg*

            Specify the optimizing *arg* for phyml. One of the following are

            allowed: *tlr*, *tl*, *lr*, *l*, *r*, or *n*. Default is *tlr*,

            optimize all.



    -p, --phyml=*arg*

            Specify the *PATH* to the phyml binary to be used. Good to use

            when creating files for the Maui batch system or for running

            files on remote systems. The default path for phyml is otherwise

            taken from the users current PATH.



    -se, --search=*arg*

            Specify the search *arg* for phyml. One of the following are

            allowed: *NNI*, *SPR*, or *BEST*. Default is *NNI*, the default

            in phyml.



    -su, --summarize

            Summarize the output from pmraic.pl/phyml. Can also be set to

            --nosummarize.



    -v, --verbose

            Be verbose. Can also be set to --noverbose.



    -h, --help

            Prints help message and exits



    -v, --version

            Prints version message and exits



    -man, --man

            Displays the manual page



USAGE



    Examples:



    Run PHYML in parallel. Default is to start as many different runs as

    number of cores available



        pmraic.pl data.dat



    Run PHYML in parallel and without asking for user input



        pmraic.pl --noverbose data.dat



    Run two instances of PHYML in parallel (12 serial PHYML runs per CPU)



        pmraic.pl --cpu=2 data.dat



    Generate six bash scripts for running serial (6X4) PHYML analyses.



        pmraic.pl --bash=6 data.dat



    Generate a Maui submit script for running PHYML on a cluster



        pmraic.pl --maui --phyml=/path/on/cluster/to/phyml data.dat



    Run four models in parallel



        pmraic.pl --models=JC69,JC69I,JC69G,JC69IG data.dat



    Run 56 models (the "Modeltest" set) in parallel



        pmraic.pl --modeltest data.dat



    Summarize output from previous run(s)



        pmraic.pl --summarize data.dat



AUTHOR



    Written by Johan A. A. Nylander



REPORTING BUGS



    See DEPENDENCIES below.

    Please report any further bugs to *jnylander @ users.sourceforge.net*.



DEPENDENCIES



    Needs PhyML v. > 3.0 to run. Note that current precompiled versions of

    PhyML ("v3.0_360-500M") available from

    http://www.atgc-montpellier.fr/phyml/ contains a bug preventing "I"

    models to be correctly analysed (alpha jointly estimated, even when not

    supposed to). This might effect model evaluations, especially if the

    program is used in "toggle mode". The bug seems to be fixed, however, in

    latest versions (at least v."20110919") available on

    http://code.google.com/p/phyml/.



    Install on Ubuntu Linux:



        sudo apt install phyml



    Uses Perl modules Pod::Usage, Parallel::ForkManager.



    Install on Ubuntu Linux:



      sudo apt install perl-doc libparallel-forkmanager-perl



    or directly from CPAN:



      sudo perl -MCPAN -e 'install Parallel::ForkManager'



LICENSE AND COPYRIGHT



    Copyright (c) 2009-2020 Johan Nylander

                   

    Permission is hereby granted, free of charge, to any person

    obtaining a copy of this software and associated documentation

    files (the "Software"), to deal in the Software without

    restriction, including without limitation the rights to use,

    copy, modify, merge, publish, distribute, sublicense, and/or

    sell copies of the Software, and to permit persons to whom the

    Software is furnished to do so, subject to the following

    conditions:



    The above copyright notice and this permission notice shall be

    included in all copies or substantial portions of the Software.



    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,

    EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES

    OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND

    NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT

    HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,

    WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING

    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR

    OTHER DEALINGS IN THE SOFTWARE.



DOWNLOAD



    https://github.com/nylander/pMrAIC