# BIONJ:
# -----------------------------------------------------
-our $BIONJ = "";
-our $BIONJ_VERSION = "";
+our $BIONJ = "";
+our $BIONJ_VERSION = "";
# WEIGHBOR:
# -----------------------------------------------------
-our $WEIGHBOR = "";
-our $WEIGHBOR_VERSION = "";
+our $WEIGHBOR = "";
+our $WEIGHBOR_VERSION = "";
# PHYML:
# -----------------------------------------------------
-our $PHYML = $SOFTWARE_DIR."PHYLO/PhyML/PhyML-3.1/PhyML-3.1/PhyML-3.1_linux64";
-our $PHYML_VERSION = "3.1";
+our $PHYML = $SOFTWARE_DIR."PHYLO/PhyML/PhyML-3.1/PhyML-3.1/PhyML-3.1_linux64";
+our $PHYML_VERSION = "3.1";
# RAXML:
# -----------------------------------------------------
-our $RAXML = $SOFTWARE_DIR."PHYLO/RAxML/20161215/standard-RAxML-master/raxmlHPC-AVX";
-our $RAXML_VERSION = "8.2.9";
+our $RAXML = $SOFTWARE_DIR."PHYLO/RAxML/20161215/standard-RAxML-master/raxmlHPC-AVX";
+our $RAXML_VERSION = "8.2.9";
# forester.jar. This jar file is currently available at: https://sites.google.com/site/cmzmasek/home/software/forester
# --------------------------------------------------------------------------------------------------------------------
-our $FORESTER_JAR = "/home/zma/git/forester/forester/java/forester.jar";
+our $FORESTER_JAR = "/home/zma/git/forester/forester/java/forester.jar";
# Tool from forester.jar to transfer support values:
# -------------------------------------------------
-our $SUPPORT_TRANSFER = $JAVA." -cp $FORESTER_JAR org.forester.application.support_transfer";
+our $SUPPORT_TRANSFER = $JAVA." -cp $FORESTER_JAR org.forester.application.support_transfer";
} ## executeProtpars
-
-# "Model of substitution" order for DQO TREE-PUZZLE 5.0:
+# "Model of substitution" order for TREE-PUZZLE 5.2:
+# For amino acids:
# Auto
# m -> Dayhoff (Dayhoff et al. 1978)
# m -> JTT (Jones et al. 1992)
# m -> VT (Mueller-Vingron 2000)
# m -> WAG (Whelan-Goldman 2000)
# m -> Auto
+#
+# For nucleotides:
+# HKY (Hasegawa et al. 1985)
+# m -> TN (Tamura-Nei 1993)
+# m -> GTR (e.g. Lanave et al. 1980)
+# m -> SH (Schoeniger-von Haeseler 1994)
+# m -> HKY (Hasegawa et al. 1985)
+#
# One argument:
-# matrix option: 0 = JTT; 2 = BLOSUM 62; 3 = mtREV24;
-# 5 = VT; 6 = WAG; 7 = auto; PAM otherwise
-# Last modified: 07/07/01
+# matrix option:
+# 0 = JTT
+# 2 = BLOSUM 62
+# 3 = mtREV24
+# 5 = VT
+# 6 = WAG
+# 7 = auto
+# 9 = HKY [na]
+# 10 = TN [na]
+# 11 = GTR [na]
+# 12 = SH [na]
+# PAM otherwise
+# Last modified: 17/04/26
sub setModelForPuzzle {
my $matrix_option = $_[ 0 ];
my $matr = "";
- if ( $matrix_option == 0 ) { # JTT
+ if ( $matrix_option == 0 || $matrix_option == 11 ) { # JTT or GTR
$matr = "
m
m";
m
m";
}
- elsif ( $matrix_option == 3 ) { # mtREV24
+ elsif ( $matrix_option == 3 || $matrix_option == 12) { # mtREV24 or SH
$matr = "
m
m
m
m";
}
- elsif ( $matrix_option == 7 ) { # auto
+ elsif ( $matrix_option == 7 || $matrix_option == 9 ) { # auto or HKY
$matr = "";
- }
+ }
+ elsif ( $matrix_option == 10 ) { # TN
+ $matr = "
+m"
+ }
else { # PAM
$matr = "
m"