From 565d0310d54ba529b128ffb34c33342e99bf6a15 Mon Sep 17 00:00:00 2001 From: Martin Wilke Date: Sat, 15 Dec 2007 15:13:41 +0000 Subject: [PATCH] MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. The conditioning is accomplished using Bayes's theorem. The posterior probability distribution of trees is impossible to calculate analytically; instead, MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. WWW: http://mrbayes.csit.fsu.edu/ PR: ports/118542 Submitted by: mzaki at biol.s.u-tokyo.ac.jp --- biology/Makefile | 1 + biology/mrbayes/Makefile | 34 ++++++++++++++++++++++++++++ biology/mrbayes/distinfo | 3 +++ biology/mrbayes/files/patch-Makefile | 11 +++++++++ biology/mrbayes/pkg-descr | 11 +++++++++ 5 files changed, 60 insertions(+) create mode 100644 biology/mrbayes/Makefile create mode 100644 biology/mrbayes/distinfo create mode 100644 biology/mrbayes/files/patch-Makefile create mode 100644 biology/mrbayes/pkg-descr diff --git a/biology/Makefile b/biology/Makefile index 9cc884558da2..3b535a3b219f 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -46,6 +46,7 @@ SUBDIR += migrate SUBDIR += molden SUBDIR += mopac + SUBDIR += mrbayes SUBDIR += mummer SUBDIR += nab SUBDIR += ncbi-toolkit diff --git a/biology/mrbayes/Makefile b/biology/mrbayes/Makefile new file mode 100644 index 000000000000..bb21910860d4 --- /dev/null +++ b/biology/mrbayes/Makefile @@ -0,0 +1,34 @@ +# New ports collection makefile for: mrbayes +# Date created: 11 December 2007 +# Whom: mzaki@biol.s.u-tokyo.ac.jp +# +# $FreeBSD$ +# + +PORTNAME= mrbayes +PORTVERSION= 3.1.2 +CATEGORIES= biology +MASTER_SITES= SF + +MAINTAINER= mzaki@biol.s.u-tokyo.ac.jp +COMMENT= Bayesian inference of phylogeny + +USE_GMAKE= yes + +LIB_DEPENDS+= readline.5:${PORTSDIR}/devel/readline + +PLIST_FILES= bin/mb + +PORTEXAMPLES= adh.nex anolis.nex avian_ovomucoids.nex bglobin.nex \ + cynmix.nex kim.nex primates.nex replicase.nex + +do-install: + @${INSTALL_PROGRAM} ${WRKSRC}/mb ${PREFIX}/bin/ +.if !defined(NOPORTEXAMPLES) + @${MKDIR} ${EXAMPLESDIR} +.for file in ${PORTEXAMPLES} + @${INSTALL_DATA} ${WRKSRC}/${file} ${EXAMPLESDIR} +.endfor +.endif + +.include diff --git a/biology/mrbayes/distinfo b/biology/mrbayes/distinfo new file mode 100644 index 000000000000..c5a7efce9b6d --- /dev/null +++ b/biology/mrbayes/distinfo @@ -0,0 +1,3 @@ +MD5 (mrbayes-3.1.2.tar.gz) = 942e4e0a90fa23481bb1f2e0fa0e0d66 +SHA256 (mrbayes-3.1.2.tar.gz) = c60253de1980c9f0a0eb684fffe7ba428fda7c39a3edcb6acf384b5e1443f2f4 +SIZE (mrbayes-3.1.2.tar.gz) = 545968 diff --git a/biology/mrbayes/files/patch-Makefile b/biology/mrbayes/files/patch-Makefile new file mode 100644 index 000000000000..eb99e4b74905 --- /dev/null +++ b/biology/mrbayes/files/patch-Makefile @@ -0,0 +1,11 @@ +--- Makefile.orig 2005-12-23 01:13:06.000000000 +0900 ++++ Makefile 2007-12-11 11:35:36.000000000 +0900 +@@ -19,7 +19,7 @@ + + # set compiler for the non-MPI version (mpicc will be used for the MPI + # version regardless of this setting) +-CC = gcc ++CC ?= gcc + + # set to yes if you want to use the readline library (make sure you have it + # installed on your machine) diff --git a/biology/mrbayes/pkg-descr b/biology/mrbayes/pkg-descr new file mode 100644 index 000000000000..11dff2bd39ca --- /dev/null +++ b/biology/mrbayes/pkg-descr @@ -0,0 +1,11 @@ +MrBayes is a program for the Bayesian estimation of phylogeny. + +Bayesian inference of phylogeny is based upon a quantity called the +posterior probability distribution of trees, which is the probability of a +tree conditioned on the observations. The conditioning is accomplished +using Bayes's theorem. The posterior probability distribution of trees is +impossible to calculate analytically; instead, MrBayes uses a simulation +technique called Markov chain Monte Carlo (or MCMC) to approximate the +posterior probabilities of trees. + +WWW: http://mrbayes.csit.fsu.edu/