Index: head/biology/paml/Makefile
===================================================================
--- head/biology/paml/Makefile	(revision 493970)
+++ head/biology/paml/Makefile	(revision 493971)
@@ -1,53 +1,54 @@
 # Created by: dbader@eece.unm.edu
 # $FreeBSD$
 
 PORTNAME=	paml
-PORTVERSION=	4.9h
+PORTVERSION=	4.9i
 CATEGORIES=	biology
 MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
 DISTNAME=	${PORTNAME}${DISTVERSION}
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)
 
 LICENSE=	GPLv3
 
 USES=		dos2unix gmake tar:tgz
+
 DOS2UNIX_GLOB=	*.HKYG5 *.aa *.c *.ctl *.dat *.nexus *.nuc *.phy *.result *.tre \
 		*.trees *.txt *.xml paupblock paupend
 
 BINARIES=	baseml basemlg chi2 codeml evolver evolverNSbranches \
 		evolverNSbranchsites evolverNSsites pamp yn00
 
 OPTIONS_DEFINE=	DOCS EXAMPLES
 
 post-extract:
 	@${FIND} ${WRKSRC}/Technical -name "*.exe" -delete
 
 do-build:
 	@cd ${WRKSRC}/src && ${SETENV} ${MAKE_ENV} ${MAKE_CMD}
 .for f in NSbranches NSsites NSbranchsites
 	@cd ${WRKSRC}/src && \
 	${CC} ${CFLAGS} -DCodon${f} -o evolver${f} evolver.c tools.c -lm
 .endfor
 
 do-install:
 .for f in ${BINARIES}
 	${INSTALL_PROGRAM} ${WRKSRC}/src/${f} ${STAGEDIR}${PREFIX}/bin
 .endfor
 
 do-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR}
 
 do-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat Technical" \
 		${STAGEDIR}${EXAMPLESDIR})
 	(cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
 .for f in *.aa *.ctl *.dat *.nuc *.trees *.txt paup*
 	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${EXAMPLESDIR}
 .endfor
 
 .include <bsd.port.mk>
Index: head/biology/paml/distinfo
===================================================================
--- head/biology/paml/distinfo	(revision 493970)
+++ head/biology/paml/distinfo	(revision 493971)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1524675240
-SHA256 (paml4.9h.tgz) = 623bf6cf4a018a4e7b4dbba189c41d6c0c25fdca3a0ae24703b82965c772edb3
-SIZE (paml4.9h.tgz) = 6241149
+TIMESTAMP = 1551192920
+SHA256 (paml4.9i.tgz) = bc11af500b88d977a8765161f6c014f178273cbd887657eebd6330a3a967b4cc
+SIZE (paml4.9i.tgz) = 6556407
Index: head/biology/paml/pkg-plist
===================================================================
--- head/biology/paml/pkg-plist	(revision 493970)
+++ head/biology/paml/pkg-plist	(revision 493971)
@@ -1,172 +1,173 @@
 %%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf
 %%PORTDOCS%%%%DOCSDIR%%/README.txt
 %%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
 %%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
 %%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/3s.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/4s.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/5s.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/6s.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/9s.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/ECP_EDN_15.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/PAMLCladeModelCDnotes.pdf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeC.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/codeml.CladeD.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/CladeModelCD/tree.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BF.Clock23.xlsx
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/BFdriverDOC.pdf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/FixedDsClock23.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.BayesFactor.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf1/mcmctree.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/bf2/mcmctree.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.Infinitesites.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mcmctree.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/DatingSoftBound/mtCDNApri123.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/GeneticCode.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/HIVenvSweden4s.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HIVNSsites/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCaa.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbase.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCbaseRandomTree.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MCcodon.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.phy
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/bigmhc.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MHC.Swanson2002MBE/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.aa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/MouseLemurs123.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/README2.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/aaml2.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/baseml2.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/codonml2.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MouseLemurs/mtmam.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/eigenQREV.pdf
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Pt/testPMat.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranches.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSbranchsites.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSclade.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/MCcodonNSsites.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/PositiveSites.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/Codon/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.c
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Technical/Simulation/multiruns.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.Nulldata.xml
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.Beast.xml
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.NodeNumbers.tre
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.nexus
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.tre
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/H1.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/baseml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/commands.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/in.BV.HKYG5
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/FigTree.tre
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/baseml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/in.BV.HKYG5
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ExactlnL.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/aaml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.aa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/baseml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.rooted.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/brown.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/codonml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dNdSGene1.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/MtZoa.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV10.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/cpREV64.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff-dcmut.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/dayhoff.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974a.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974c.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974p.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/g1974v.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/grantham.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones-dcmut.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/jones.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/lg.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/miyata.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtArt.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtREV24.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/mtmam.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dat/wag.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/horai.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/RasMol.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/SiteNumbering.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/codemlYangSwanson2002.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysin.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysin/lysinYangSwanson2002.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeLarge.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/lysozyme/lysozymeSmall.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mcmctree.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/AAcodon.result.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.AAcodon.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/miyata.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNAmam.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.aa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNA/mtCDNApri.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/2s.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/OmegaAA.dat
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/README.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.HC.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/codeml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNA.HC.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupstart
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.aa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/yn00.ctl
 bin/baseml
 bin/basemlg
 bin/chi2
 bin/codeml
 bin/evolver
 bin/evolverNSbranches
 bin/evolverNSbranchsites
 bin/evolverNSsites
 bin/pamp
 bin/yn00