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-rw-r--r--academic/PhyML/20131112.patch (renamed from academic/PhyML/20130219.patch)90
-rw-r--r--academic/PhyML/PhyML.SlackBuild35
-rw-r--r--academic/PhyML/PhyML.info4
-rw-r--r--academic/PhyML/README2
-rw-r--r--academic/PhyML/References4
5 files changed, 117 insertions, 18 deletions
diff --git a/academic/PhyML/20130219.patch b/academic/PhyML/20131112.patch
index 59250c71db..e7eb2670b6 100644
--- a/academic/PhyML/20130219.patch
+++ b/academic/PhyML/20131112.patch
@@ -1,5 +1,4 @@
-Common subdirectories: ./phyml-20120412/src/.deps and ./phyml-20120412-new-bak/src/.deps
-diff -uN ./phyml-20120412/src/help.c ./phyml-20120412-new-bak/src/help.c
+unchanged:
--- ./phyml-20120412/src/help.c 2011-09-22 14:51:57.000000000 +1200
+++ ./phyml-20120412-new-bak/src/help.c 2013-02-18 21:51:51.448662440 +1300
@@ -96,7 +96,7 @@
@@ -11,7 +10,7 @@ diff -uN ./phyml-20120412/src/help.c ./phyml-20120412-new-bak/src/help.c
PhyML_Printf("%s\t\tChanges interleaved format (default) to sequential format.\n",FLAT);
PhyML_Printf("\n");
-diff -uN ./phyml-20120412/src/lk.c ./phyml-20120412-new-bak/src/lk.c
+unchanged:
--- ./phyml-20120412/src/lk.c 2012-04-05 14:47:37.000000000 +1200
+++ ./phyml-20120412-new-bak/src/lk.c 2013-02-19 10:22:22.665284529 +1300
@@ -472,7 +472,7 @@
@@ -217,7 +216,7 @@ diff -uN ./phyml-20120412/src/lk.c ./phyml-20120412-new-bak/src/lk.c
if(p_lk[site*NsNg+catg*Ns+i] < smallest_p_lk) smallest_p_lk = p_lk[site*NsNg+catg*Ns+i] ;
}
-diff -uN ./phyml-20120412/src/Makefile ./phyml-20120412-new-bak/src/Makefile
+unchanged:
--- ./phyml-20120412/src/Makefile 1970-01-01 12:00:00.000000000 +1200
+++ ./phyml-20120412-new-bak/src/Makefile 2013-02-18 21:54:46.957806553 +1300
@@ -0,0 +1,1082 @@
@@ -1303,7 +1302,7 @@ diff -uN ./phyml-20120412/src/Makefile ./phyml-20120412-new-bak/src/Makefile
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
-diff -uN ./phyml-20120412/src/mcmc.c ./phyml-20120412-new-bak/src/mcmc.c
+unchanged:
--- ./phyml-20120412/src/mcmc.c 2012-03-20 14:10:49.000000000 +1300
+++ ./phyml-20120412-new-bak/src/mcmc.c 2013-02-18 21:51:51.459662430 +1300
@@ -1977,7 +1977,7 @@
@@ -1315,7 +1314,7 @@ diff -uN ./phyml-20120412/src/mcmc.c ./phyml-20120412-new-bak/src/mcmc.c
else
{
For(i,tree->mod->n_catg) PhyML_Fprintf(fp,"%G\t",tree->mod->gamma_r_proba->v[i]);
-diff -uN ./phyml-20120412/src/optimiz.c ./phyml-20120412-new-bak/src/optimiz.c
+unchanged:
--- ./phyml-20120412/src/optimiz.c 2012-03-13 19:04:03.000000000 +1300
+++ ./phyml-20120412-new-bak/src/optimiz.c 2013-02-18 21:51:51.462662427 +1300
@@ -979,29 +979,18 @@
@@ -1355,13 +1354,13 @@ diff -uN ./phyml-20120412/src/optimiz.c ./phyml-20120412-new-bak/src/optimiz.c
tree->mod->gamma_r_proba_unscaled->v[tree->mod->n_catg-1] = 100.;
For(i,tree->mod->n_catg-1)
-diff -uN ./phyml-20120412/src/tree ./phyml-20120412-new-bak/src/tree
+unchanged:
--- ./phyml-20120412/src/tree 1970-01-01 12:00:00.000000000 +1200
+++ ./phyml-20120412-new-bak/src/tree 2013-02-19 10:09:36.962892889 +1300
@@ -0,0 +1 @@
+((((((tax6:0.01,(tax5:0.01,tax1:0.026):0.008):0.003,(tax7:0.003,tax3:0.003):0.01271127):0.01,tax2:0.01):0.01,tax10:0.01):0.01,tax9:0.01):0.01,tax8:0.01,tax4:0.1);
\ No newline at end of file
-diff -uN ./phyml-20120412/src/utilities.c ./phyml-20120412-new-bak/src/utilities.c
+unchanged:
--- ./phyml-20120412/src/utilities.c 2012-04-11 11:48:30.000000000 +1200
+++ ./phyml-20120412-new-bak/src/utilities.c 2013-02-19 10:16:57.770281203 +1300
@@ -1668,6 +1668,7 @@
@@ -1505,7 +1504,7 @@ diff -uN ./phyml-20120412/src/utilities.c ./phyml-20120412-new-bak/src/utilities
list = (t_node ***)mCalloc(node_list_size,sizeof(t_node **));
For(i,node_list_size) list[i] = (t_node **)mCalloc(2*tree->n_otu-1,sizeof(t_node *));
size = (int *)mCalloc(node_list_size,sizeof(int));
-diff -uN ./phyml-20120412/src/utilities.h ./phyml-20120412-new-bak/src/utilities.h
+unchanged:
--- ./phyml-20120412/src/utilities.h 2012-04-11 11:39:02.000000000 +1200
+++ ./phyml-20120412-new-bak/src/utilities.h 2013-02-18 21:51:51.452662435 +1300
@@ -272,6 +272,8 @@
@@ -1517,3 +1516,76 @@ diff -uN ./phyml-20120412/src/utilities.h ./phyml-20120412-new-bak/src/utilities
/*!********************************************************/
+unchanged:
+--- utilities.c 2013-10-31 08:57:09.622430940 +1300
++++ utilities.new.c 2013-10-31 08:55:49.522433717 +1300
+@@ -4769,8 +4769,6 @@
+ t_node *n_e, *n_f;
+
+ n_otu = t_full->n_otu;
+- t_empt->n_root = t_full->n_root;
+- t_empt->e_root = t_full->e_root;
+ t_empt->c_lnL_sorted = t_full->c_lnL_sorted;
+ t_empt->log_site_lk_cat = t_full->log_site_lk_cat;
+ t_empt->cur_site_lk = t_full->cur_site_lk;
+@@ -6993,6 +6991,7 @@
+ boot_tree->mat = boot_mat;
+ }
+
++
+ boot_tree->mod = boot_mod;
+ boot_tree->io = tree->io;
+ boot_tree->data = boot_data;
+@@ -7002,6 +7001,7 @@
+ boot_tree->io->print_site_lnl = 0;
+ boot_tree->io->print_trace = 0;
+
++
+ if((boot_tree->mod->s_opt->random_input_tree) && (boot_tree->mod->s_opt->topo_search == SPR_MOVE)) Random_Tree(boot_tree);
+ Order_Tree_CSeq(boot_tree,boot_data);
+ Share_Lk_Struct(tree,boot_tree);
+@@ -7010,6 +7010,7 @@
+ Fill_Dir_Table(boot_tree);
+ Update_Dirs(boot_tree);
+
++
+ if(tree->mod->s_opt->greedy) Init_P_Lk_Tips_Double(boot_tree);
+ else Init_P_Lk_Tips_Int(boot_tree);
+ Init_Ui_Tips(boot_tree);
+@@ -13307,11 +13308,15 @@
+ Warn_And_Exit("");
+ }
+
++ has_outgrp = NO;
++
++ /* 'Root' node is t_nodes[0] */
+ if(strstr(tree->t_nodes[0]->name,"*"))
+ {
+ /* PhyML_Printf("\n. Found outgroup taxon: %s",tree->t_nodes[0]->name); */
+ tree->t_nodes[0]->s_ingrp[0] = 0;
+ tree->t_nodes[0]->s_outgrp[0] = 1;
++ has_outgrp = YES;
+ }
+ else
+ {
+@@ -13319,7 +13324,6 @@
+ tree->t_nodes[0]->s_outgrp[0] = 0;
+ }
+
+- has_outgrp = NO;
+ Get_Best_Root_Position_Post(tree->t_nodes[0],tree->t_nodes[0]->v[0],&has_outgrp,tree);
+ Get_Best_Root_Position_Pre(tree->t_nodes[0],tree->t_nodes[0]->v[0],tree);
+
+only in patch2:
+unchanged:
+--- src/utilities.c 2012-04-11 11:48:30.000000000 +1200
++++ src.new/utilities.c 2013-11-12 14:19:11.600689913 +1300
+@@ -13995,7 +13995,7 @@ int Check_Topo_Constraints(t_tree *big_t
+ For(i,2*big_tree_cpy->n_otu-3) big_tree_cpy->t_edges[i]->bip_score = 0;
+ For(i,2*small_tree->n_otu-3) small_tree->t_edges[i]->bip_score = 0;
+
+- diffs = Compare_Bip(small_tree,big_tree_cpy,YES);
++ diffs = Compare_Bip(small_tree,big_tree_cpy,NO);
+
+ /* printf("\n"); */
+ /* printf("\n. %s",Write_Tree(big_tree_cpy,NO)); */
diff --git a/academic/PhyML/PhyML.SlackBuild b/academic/PhyML/PhyML.SlackBuild
index 9946b20954..3578b7288c 100644
--- a/academic/PhyML/PhyML.SlackBuild
+++ b/academic/PhyML/PhyML.SlackBuild
@@ -2,7 +2,7 @@
# Slackware build script for PhyML
-# Copyright 2011-2013 Petar Petrov, ppetrov@paju.oulu.fi
+# Copyright 2011-2013 Petar Petrov, petar.petrov@student.oulu.fi
# All rights reserved.
#
# Redistribution and use of this script, with or without modification, is
@@ -25,7 +25,7 @@
# Thanks to Niels Horn for some handy modifications and corrections.
PRGNAM=PhyML
-VERSION=${VERSION:-20130219}
+VERSION=${VERSION:-20131112}
BUILD=${BUILD:-1}
TAG=${TAG:-_SBo}
@@ -69,16 +69,17 @@ tar xvf $CWD/$SRCNAM-$SRCVER.tar.gz
cd $SRCNAM-$SRCVER
chown -R root:root .
find -L . \
- \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 -o -perm 511 \) \
- -exec chmod 755 {} \; -o \
- \( -perm 666 -o -perm 664 -o -perm 600 -o -perm 444 -o -perm 440 -o -perm 400 \) \
- -exec chmod 644 {} \;
+ \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \
+ -o -perm 511 \) -exec chmod 755 {} \; -o \
+ \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
-# Apply patch 20130219
+# Apply version patch
cd src
patch -i $CWD/$VERSION.patch
cd ..
+# This is PhyML
./configure \
--prefix=/usr \
--libdir=/usr/lib${LIBDIRSUFFIX} \
@@ -97,6 +98,26 @@ CXXFLAGS="$SLKCFLAGS" \
make
make install DESTDIR=$PKG
+# And this is PhyTime
+./configure \
+ --prefix=/usr \
+ --libdir=/usr/lib${LIBDIRSUFFIX} \
+ --sysconfdir=/etc \
+ --localstatedir=/var \
+ --enable-phytime \
+ --mandir=/usr/man \
+ --docdir=/usr/doc/$PRGNAM-$VERSION \
+ --build=$ARCH-slackware-linux
+
+# Use our CFLAGS
+sed -i "/^CFLAGS/s/=/+=/" src/Makefile
+sed -i "/^CFLAGS/s/=/+=/" Makefile
+
+CFLAGS="$SLKCFLAGS" \
+CXXFLAGS="$SLKCFLAGS" \
+make
+make install DESTDIR=$PKG
+
find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
| cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true
diff --git a/academic/PhyML/PhyML.info b/academic/PhyML/PhyML.info
index 52478c9962..e37d35be73 100644
--- a/academic/PhyML/PhyML.info
+++ b/academic/PhyML/PhyML.info
@@ -1,5 +1,5 @@
PRGNAM="PhyML"
-VERSION="20130219"
+VERSION="20131112"
HOMEPAGE="http://code.google.com/p/phyml/"
DOWNLOAD="http://phyml.googlecode.com/files/phyml-20120412.tar.gz"
MD5SUM="d2207a3d6caf633c43239a01ce70f244"
@@ -7,4 +7,4 @@ DOWNLOAD_x86_64=""
MD5SUM_x86_64=""
REQUIRES=""
MAINTAINER="Petar Petrov"
-EMAIL="ppetrov@paju.oulu.fi"
+EMAIL="petar.petrov@student.oulu.fi"
diff --git a/academic/PhyML/README b/academic/PhyML/README
index b52080e622..60178833a8 100644
--- a/academic/PhyML/README
+++ b/academic/PhyML/README
@@ -9,6 +9,8 @@ It also implements two methods to evaluate branch supports in a sound
statistical framework (the non-parametric bootstrap and the
approximate likelihood ratio test).
+The script also builds the additional program PhyTime.
+
For details and citation
New Algorithms and Methods to Estimate Maximum-Likelihood
Phylogenies: Assessing the Performance of PhyML 3.0. Guindon S.,
diff --git a/academic/PhyML/References b/academic/PhyML/References
index 17fd35add2..41f1be6bb2 100644
--- a/academic/PhyML/References
+++ b/academic/PhyML/References
@@ -2,3 +2,7 @@ New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies:
Assessing the Performance of PhyML 3.0. Guindon S., Dufayard J.F.,
Lefort V., Anisimova M., Hordijk W., Gascuel O. Systematic Biology,
59(3):307-21, 2010.
+
+Bayesian estimation of divergence times from large sequence alignments.
+Mol Biol Evol. 2010 Aug;27(8):1768-81. doi: 10.1093/molbev/msq060.
+Epub 2010 Mar 1.