[med-svn] r14294 - trunk/packages/phyml/trunk/debian

Wed Jul 31 11:44:24 UTC 2013

Author: tille
Date: 2013-07-31 11:44:24 +0000 (Wed, 31 Jul 2013)
New Revision: 14294

Added:
   trunk/packages/phyml/trunk/debian/phytime.1
Modified:
   trunk/packages/phyml/trunk/debian/changelog
Log:
Manpage for phytime


Modified: trunk/packages/phyml/trunk/debian/changelog
===================================================================

--- trunk/packages/phyml/trunk/debian/changelog	2013-07-31 11:38:54 UTC (rev 14293)
+++ trunk/packages/phyml/trunk/debian/changelog	2013-07-31 11:44:24 UTC (rev 14294)
@@ -14,6 +14,8 @@
      - Use dh more consequently to work around two different configure steps
      - Propagate hardening options
   * debian/upstream: Additional (newer) publication
+  * debian/phytime.1: Add manpage for phytime based on some html2man output
+    and the abstract of the according publication
 
  -- Charles Plessy <plessy at debian.org>  Mon, 15 Jul 2013 09:55:11 +0900
 

Added: trunk/packages/phyml/trunk/debian/phytime.1
===================================================================
--- trunk/packages/phyml/trunk/debian/phytime.1	                        (rev 0)
+++ trunk/packages/phyml/trunk/debian/phytime.1	2013-07-31 11:44:24 UTC (rev 14294)
@@ -0,0 +1,173 @@
+.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 ouput 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.
+


