biology/paml: Update to version 4.9i

Upstream changes as described by the author:

- mcmctree: I have added an option (duplication = 1) for dating a tree with
both speciations and gene duplications, so that some nodes on the tree
share divergence times. Nodes sharing ages are identified using labels in
the tree file: #1, #2, .... I have yet to update the document about
specification of the model.

- mcmctree: The TipDate option was written for one locus or partition and
never worked for more than two loci/partitions. I have edited the code so
that it works for multiple partitions, some of which may be molecular and
the others morphological.

- codeml: The option estFreq = 0 when codonFreq = 6 (FMutSel0) and 7
(FMutSel) is not working in versions 4.9g and 4.9h. This is fixed now. This
option uses the observed codon or amino acid frequencies for the
mutation-selection models of codon usage. Instead the program estimates the
frequencies using maximum likeihood, which is what the option estFreq = 1
does. Look at the README file in the examples/mtCDNAape/ folder.

- codeml clade model D: The bounds for the w (dN/dS) ratios in the first
site classes are set tp (0.0001, 0.5) for w0 and (0.5, 1.5) for w1, in
versions 4.9b,c,d,e,f,g, since I added the BEB calculation for clade model
D in 4.9b. The motivation for the bounds is that site class 0 represents
strong purifying selection with a small w0, while site class 1 should
include sites under weak purifying selection with a larger w1. However the
bounds are arbitrary. In some datasets, the MLEs are found to be at the
bounds, making the interpretation awkward. I have changed the bounds to the
following: w0b[]={0.0001, 1.0}, w1b[]={0.01, 1.5}. This means that the user
should swap the estimates of w0 and w2 if w0 > w1.

3 files changed, 6 insertions, 4 deletions

diff --git a/biology/paml/Makefile b/biology/paml/Makefile
index 7cfbe87f31ad..9935a1ee5ab8 100644
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@@ -2,7 +2,7 @@
 # $FreeBSD$
 
 PORTNAME=	paml
-PORTVERSION=	4.9h
+PORTVERSION=	4.9i
 CATEGORIES=	biology
 MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
 DISTNAME=	${PORTNAME}${DISTVERSION}
@@ -13,6 +13,7 @@ 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
 
diff --git a/biology/paml/distinfo b/biology/paml/distinfo
index 0cbd1225cbc1..3a3170b734b9 100644
--- a/biology/paml/distinfo
+++ b/biology/paml/distinfo
@@ -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
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
index 935696c9cea1..9c0041d7c15f 100644
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@@ -77,6 +77,7 @@
 %%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