[Debian-med-packaging] MP patch for PhyML

Tue Feb 15 07:04:10 UTC 2011

Hi Stephane,

thanks for your quick response.  I wonder if David as the author of this
MP patch would be willing to provide it for the latest development
release (because I personally do not use phyml and do not even have an
idea how to test it).  I'm volunteering to provide help (perhaps via the
competence of the Debian mailing list in build system questions.

For the moment I can provide a phyml.1 manpage (attached).  Feel free to
(change and) include it into your official PhyML code.

Kind regards

       Andreas.

On Tue, Feb 15, 2011 at 02:51:35PM +1300, Stephane Guindon wrote:
> 
> Dear Andreas,
> 
> Thank you very much for contributing to PhyML.
> Yes, it makes perfect sense to try and include this functionality
> into the latest release of the program. Please feel free to take
> a look at the most recent version of the sources on our svn server
> (http://code.google.com/p/phyml/source/browse/#svn%2Ftrunk%2Fsrc)
> and let me know how to amend the configure.ac, *.c  and *.h file
> in an appropriate manner.
> 
> Regards,
> 
> -Stephane-
> 
> On 15/02/11 03:26, Andreas Tille wrote:
> > Hi PhyML authors,
> > 
> > when discssing with Diego about a program which uses PhyML he told me
> > about his MP patch which would enable making use of hybrid memory when
> > running PhyML on clusters.  I was considering to port this patch to the
> > Debian packaged version where I intended to support two versions of
> > the package: one conventional phylip and one phylip-mp.
> > 
> > When inspecting the patch I noticed that it was done against an older
> > version of PhyML (20100123).  I would consider it a reasonable idea if
> > this patch would be included into the upstream version by just wrapping
> > it into "#ifdef"s properly to enable switching between both versions by
> > simply providing different options to make.  If the patch would be taken
> > over into the official PhyML code this would simplify our work as
> > distributor (as well as Diego's work) and it might be of extra value for
> > other users.
> > 
> > What do you think about this idea?
> > 
> > Kind regards
> > 
> >       Andreas.
> > 
> 
> -- 
> Stephane Guindon
> Department of Statistics
> University of Auckland
> http://www.stat.auckland.ac.nz
> 

-- 
http://fam-tille.de
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.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\-\-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 <tille at debian.org>,
for the Debian project (but may be used by others).