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commit d1686531247f8221765a19b889172b15ce151185 Author: Andreas Tille <[email protected]> Date: Tue Jun 27 15:06:48 2017 +0200 Do not build phytime since it is not supported any more --- debian/changelog | 1 + debian/phytime.1 | 173 ------------------------------------------------------- debian/rules | 2 + 3 files changed, 3 insertions(+), 173 deletions(-) diff --git a/debian/changelog b/debian/changelog index 3d70393..8da3efd 100644 --- a/debian/changelog +++ b/debian/changelog @@ -5,6 +5,7 @@ phyml (3:3.3.20170530+dfsg-1) UNRELEASED; urgency=medium * Standards-Version: 4.0.0 (no changes needed) * Do not disable PIE Closes: #865654 + * Do not build phytime since it is not supported any more -- Andreas Tille <[email protected]> Tue, 27 Jun 2017 13:20:47 +0200 diff --git a/debian/phytime.1 b/debian/phytime.1 deleted file mode 100644 index fd512aa..0000000 --- a/debian/phytime.1 +++ /dev/null @@ -1,173 +0,0 @@ -.TH PHYTIME "1" "July 2013" "phytime " "User Commands" -.SH NAME -phytime \- Bayesian estimation of divergence times from large sequence alignments -.SH DESCRIPTION -Bayesian estimation of divergence times from molecular sequences relies -on sophisticated Markov chain Monte Carlo techniques, and -Metropolis-Hastings (MH) samplers have been successfully used in that -context. This approach involves heavy computational burdens that can -hinder the analysis of large phylogenomic data sets. Reliable estimation -of divergence times can also be extremely time consuming, if not -impossible, for sequence alignments that convey weak or conflicting -phylogenetic signals, emphasizing the need for more efficient sampling -methods. This article describes a new approach that estimates the -posterior density of substitution rates and node times. The prior -distribution of rates accounts for their potential autocorrelation along -lineages, whereas priors on node ages are modeled with uniform -densities. Also, the likelihood function is approximated by a -multivariate normal density. The combination of these components leads -to convenient mathematical simplifications, allowing the posterior -distribution of rates and times to be estimated using a Gibbs sampling -algorithm. The analysis of four real-world data sets shows that this -sampler outperforms the standard MH approach and demonstrates the -suitability of this new method for analyzing large and/or difficult data -sets. -.SH SYNOPSIS -.B phytime -[command args] -.SH OPTIONS -All the options below are optional except '\-i','\-u' and '\-\-calibration'. -.PP -Command options: -.IP -\-i (or \fB\-\-input\fR) seq_file_name -.IP -seq_file_name is the name of the nucleotide or amino\-acid sequence file in PHYLIP format. -.PP - -.HP -\fB\-d\fR (or \fB\-\-datatype\fR) data_type -.IP -data_type 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) -.PP - Changes interleaved format (default) to sequential format. -.PP - -.HP -\fB\-m\fR (or \fB\-\-model\fR) model -.IP -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, 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 -\- Amino\-acid based models : LG (default) | WAG | JTT | MtREV | Dayhoff | DCMut | RtREV | CpREV | VT -.TP -Blosum62 | MtMam | MtArt | HIVw | -HIVb | custom -.PP - -.HP -\fB\-\-aa_rate_file\fR filename -.IP -filename 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\-\-calibration\fR filename -.IP -filename is the name of the calibration file that provides a priori defined boundaries for node ages. -Please read the manual for more information about the format of this file. -.PP - -.HP -\fB\-t\fR (or \fB\-\-ts\fR/tv) ts/tv_ratio -.IP -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. -.PP - -.HP -\fB\-v\fR (or \fB\-\-pinv\fR) prop_invar -.IP -prop_invar : proportion of invariable sites. -Can be a fixed value in the [0,1] range or e to get the maximum likelihood estimate. -.PP - -.HP -\fB\-c\fR (or \fB\-\-nclasses\fR) nb_subst_cat -.IP -nb_subst_cat : number of relative substitution rate categories. Default : nb_subst_cat=4. -Must be a positive integer. -.PP - -.HP -\fB\-a\fR (or \fB\-\-alpha\fR) gamma -.IP -gamma : distribution of the gamma distribution shape parameter. -Can be a fixed positive value or e to get the maximum likelihood estimate. -.PP - -.HP -\fB\-u\fR (or \fB\-\-inputtree\fR) user_tree_file -.IP -user_tree_file : starting tree filename. The tree must be in Newick format. -.PP - -.HP -\fB\-\-r_seed\fR num -.IP -num is the seed used to initiate the random number generator. -Must be an integer. -.PP - -.HP -\fB\-\-run_id\fR ID_string -.IP -Append the string ID_string 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 output otherwise. -.PP - -.HP -\fB\-\-chain_len\fR num -.IP -num is the number of generations or runs of the Markov Chain Monte Carlo. Set to 1E+6 by default. -Must be an integer. -.PP - -.HP -\fB\-\-sample_freq\fR num -.IP -The chain is sampled every num generations. Set to 1E+3 by default. -Must be an integer. -.PP - -.HP -\fB\-\-no_data\fR -.IP -Use this option to sample from the priors only (rather from the posterior joint density -of the model parameters). -.PP - -.HP -\fB\-\-fastlk\fR -.IP -Use the multivariate normal approximation to the likelihood and speed up calculations -.SH SEE ALSO -.PP - 'Bayesian estimation of divergence times from large sequence alignments.' - Stephane Guindon, - Molecular Biology and Evolution 27(8):1768\-81, 2010. -.PP - Please cite this paper if you use this software in your publications. - diff --git a/debian/rules b/debian/rules index ec6e68b..e2cdf36 100755 --- a/debian/rules +++ b/debian/rules @@ -40,9 +40,11 @@ endif # move phyml binary to temporary dir inside debian/ # mkdir -p $(CURDIR)/debian/bin mv src/phyml-mpi $(CURDIR)/debian/bin/phyml-mpi +ifeq ($(BUILDPHYTIME), 'yes') $(MAKE) distclean dh_auto_configure -- --enable-phytime dh_auto_build -- LDFLAGS="$(LDFLAGS)" CPPFLAGS="-DPHYREX $(CPPFLAGS)" +endif mv phyml-manual.pdf doc override_dh_auto_install: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phyml.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
