[med-svn] [Git][med-team/tree-puzzle][master] Reduce decimals for testing
Pranav Ballaney
gitlab at salsa.debian.org
Thu Jun 11 00:53:39 BST 2020
Pranav Ballaney pushed to branch master at Debian Med / tree-puzzle
Commits:
0e46614b by Pranav Ballaney at 2020-06-11T05:22:18+05:30
Reduce decimals for testing
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/reduce_decimals_for_testing.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+tree-puzzle (5.3~rc16+dfsg-3) UNRELEASED; urgency=medium
+
+ * Update changelog to fix a bug
+ * Reduce decimals for testing (Closes: #960760)
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com> Thu, 11 Jun 2020 05:21:30 +0530
+
tree-puzzle (5.3~rc16+dfsg-2) unstable; urgency=medium
[ Chris Lamb ]
=====================================
debian/patches/reduce_decimals_for_testing.patch
=====================================
@@ -0,0 +1,2587 @@
+Description: Reduce decimals for testing
+ Tests often fail because the last few decimals of the output
+ depend on the compiler. This patch circumvents that.
+Author: Pranav Ballaney <ballaneypranav at gmail.com>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960760
+Last-Update: 2020-06-11
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- a/tests/check-cons-pure-prot
++++ b/tests/check-cons-pure-prot
+@@ -129,17 +129,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644
+-HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187
+-HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730
+-HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172
+-MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386
+-GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272
+-LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000
+-
+-Average distance (over all possible pairs of sequences): 1.73823
+- minimum : 0.12147, maximum : 2.86187
+- variance : 0.65214, std.dev. : 0.80755
++HBB_HUMAN 0.00 0.17 0.96 0.99 2.12 1.77 2.78
++HBB_HORSE 0.17 0.00 1.01 1.02 2.09 1.78 2.86
++HBA_HUMAN 0.96 1.01 0.00 0.12 1.93 1.30 2.54
++HBA_HORSE 0.99 1.02 0.12 0.00 2.00 1.39 2.51
++MYG_PHYCA 2.12 2.09 1.93 2.00 0.00 2.12 2.79
++GLB5_PETMA 1.77 1.78 1.30 1.39 2.12 0.00 2.18
++LGB2_LUPLU 2.78 2.86 2.54 2.51 2.79 2.18 0.00
++
++Average distance (over all possible pairs of sequences): 1.73
++ minimum : 0.12, maximum : 2.86
++ variance : 0.65, std.dev. : 0.80
+
+
+ RATE HETEROGENEITY
+@@ -188,21 +188,21 @@ The following bipartitions occured at le
+ Bipartitions included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- **..*** : 100 (1.000)
+- ****... : 100 (1.000)
+- **..... : 100 (1.000)
++ **..*** : 100 (1.00)
++ ****... : 100 (1.00)
++ **..... : 100 (1.00)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****..* : 40 (0.400)
++ ****..* : 40 (0.40)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *****.. : 37 (0.370)
+- ****.*. : 23 (0.230)
++ *****.. : 37 (0.37)
++ ****.*. : 23 (0.23)
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
+@@ -227,21 +227,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04834 0.03148 8 0.28040 0.08746
+-HBB_HORSE 2 0.12685 0.03876 9 0.40362 0.12823
+-HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281
+-HBA_HORSE 4 0.09440 0.03145
+-MYG_PHYCA 5 1.33099 0.21112
+-GLB5_PETMA 6 0.70102 0.14139 10 iterations until convergence
+-LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50
++HBB_HUMAN 1 0.04 0.03 8 0.28 0.08
++HBB_HORSE 2 0.12 0.03 9 0.40 0.12
++HBA_HUMAN 3 0.02 0.02 10 0.60 0.11
++HBA_HORSE 4 0.09 0.03
++MYG_PHYCA 5 1.33 0.21
++GLB5_PETMA 6 0.70 0.14 10 iterations until convergence
++LGB2_LUPLU 7 1.76 0.28 log L: -1699.50
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04834,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440)100:0.28040,
+-(MYG_PHYCA:1.33099,GLB5_PETMA:0.70102,LGB2_LUPLU:1.76831)100:0.40362)
+-100:0.60481,HBB_HORSE:0.12685);
++(HBB_HUMAN:0.04,((HBA_HUMAN:0.02,HBA_HORSE:0.09)100:0.28,
++(MYG_PHYCA:1.33,GLB5_PETMA:0.70,LGB2_LUPLU:1.76)100:0.40)
++100:0.60,HBB_HORSE:0.12);
+
+
+ TIME STAMP
+--- a/tests/check-lm-pure-prot
++++ b/tests/check-lm-pure-prot
+@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644
+-HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187
+-HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730
+-HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172
+-MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386
+-GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272
+-LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000
++HBB_HUMAN 0.00 0.17 0.96 0.99 2.12 1.77 2.78
++HBB_HORSE 0.17 0.00 1.01 1.02 2.09 1.78 2.86
++HBA_HUMAN 0.96 1.01 0.00 0.12 1.93 1.30 2.54
++HBA_HORSE 0.99 1.02 0.12 0.00 2.00 1.39 2.51
++MYG_PHYCA 2.12 2.09 1.93 2.00 0.00 2.12 2.79
++GLB5_PETMA 1.77 1.78 1.30 1.39 2.12 0.00 2.18
++LGB2_LUPLU 2.78 2.86 2.54 2.51 2.79 2.18 0.00
+
+-Average distance (over all possible pairs of sequences): 1.73823
+- minimum : 0.12147, maximum : 2.86187
+- variance : 0.65214, std.dev. : 0.80755
++Average distance (over all possible pairs of sequences): 1.73
++ minimum : 0.12, maximum : 2.86
++ variance : 0.65, std.dev. : 0.80
+
+
+ RATE HETEROGENEITY
+--- a/tests/check-qp-clock
++++ b/tests/check-qp-clock
+@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+
+ Rate matrix R (parameters restricted to selected model):
+
+- A-C rate: 1.00000
+- A-G rate: 2.98614
+- A-T rate: 1.00000
+- C-G rate: 1.00000
+- C-T rate: 2.98614
+- G-T rate: 1.00000
++ A-C rate: 1.00
++ A-G rate: 2.98
++ A-T rate: 1.00
++ C-G rate: 1.00
++ C-T rate: 2.98
++ G-T rate: 1.00
+
+ Nucleotide frequencies (estimated from data set):
+
+@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 8
+-Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246
+- 0.23734
+-Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008
+- 0.29786
+-Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801
+- 0.23883
+-Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041
+- 0.27215
+-Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562
+- 0.27148
+-Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036
+- 0.33042
+-Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000
+- 0.22452
+-Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452
+- 0.00000
+-
+-Average distance (over all possible pairs of sequences): 0.25459
+- minimum : 0.13169, maximum : 0.33871
+- variance : 0.00207, std.dev. : 0.04544
++Thylacinus 0.00 0.25 0.22 0.24 0.26 0.24 0.22
++ 0.23
++Sarcophilu 0.25 0.00 0.13 0.26 0.28 0.32 0.26
++ 0.29
++Dasyurus 0.22 0.13 0.00 0.20 0.24 0.25 0.17
++ 0.23
++Echymipera 0.24 0.26 0.20 0.00 0.29 0.33 0.23
++ 0.27
++Trichosuru 0.26 0.28 0.24 0.29 0.00 0.21 0.28
++ 0.27
++Phalanger 0.24 0.32 0.25 0.33 0.21 0.00 0.29
++ 0.33
++Philander 0.22 0.26 0.17 0.23 0.28 0.29 0.00
++ 0.22
++Bos 0.23 0.29 0.23 0.27 0.27 0.33 0.22
++ 0.00
++
++Average distance (over all possible pairs of sequences): 0.25
++ minimum : 0.13, maximum : 0.33
++ variance : 0.00, std.dev. : 0.04
+
+
+ RATE HETEROGENEITY
+@@ -239,40 +239,40 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****..** : 999 (0.999)
+- *..***** : 999 (0.999)
+- *...**.. : 730 (0.730)
+- ******.. : 711 (0.711)
++ ****..** : 999 (0.99)
++ *..***** : 999 (0.99)
++ *...**.. : 730 (0.73)
++ ******.. : 711 (0.71)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *...**** : 466 (0.466)
++ *...**** : 466 (0.46)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ***.**.. : 333 (0.333)
+- *...**.* : 171 (0.171)
+- ***.**.* : 89 (0.089)
+- *..***.. : 80 (0.080)
+- *.....** : 79 (0.079)
+- *..*..** : 69 (0.069)
+- ****..*. : 51 (0.051)
+- *......* : 34 (0.034)
+- *..***.* : 30 (0.030)
+- ****.... : 28 (0.028)
+- ***.***. : 27 (0.027)
+- *..*.... : 22 (0.022)
+- *...***. : 20 (0.020)
+- ***..... : 19 (0.019)
+- *.....*. : 14 (0.014)
+- *..****. : 9 (0.009)
+- *..*..*. : 8 (0.008)
+- ***...** : 6 (0.006)
+- ***....* : 4 (0.004)
+- ****.**. : 1 (0.001)
++ ***.**.. : 333 (0.33)
++ *...**.* : 171 (0.17)
++ ***.**.* : 89 (0.08)
++ *..***.. : 80 (0.08)
++ *.....** : 79 (0.07)
++ *..*..** : 69 (0.06)
++ ****..*. : 51 (0.05)
++ *......* : 34 (0.03)
++ *..***.* : 30 (0.03)
++ ****.... : 28 (0.02)
++ ***.***. : 27 (0.02)
++ *..*.... : 22 (0.02)
++ *...***. : 20 (0.02)
++ ***..... : 19 (0.01)
++ *.....*. : 14 (0.01)
++ *..****. : 9 (0.00)
++ *..*..*. : 8 (0.00)
++ ***...** : 6 (0.00)
++ ***....* : 4 (0.00)
++ ****.**. : 1 (0.00)
+
+ (1 other less frequent bipartitions not shown)
+
+@@ -301,22 +301,22 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382
+-Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452
+-Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513
+-Echymipera 4 0.13997 0.04108 12 0.05457 0.02998
+-Trichosuru 5 0.10654 0.03770
+-Phalanger 6 0.12258 0.04064
+-Philander 7 0.08995 0.03428 8 iterations until convergence
+-Bos 8 0.13479 0.04095 log L: -603.37
++Thylacinus 1 0.11 0.03 9 0.05 0.03
++Sarcophilu 2 0.13 0.03 10 0.08 0.03
++Dasyurus 3 0.00 0.01 11 0.04 0.02
++Echymipera 4 0.13 0.04 12 0.05 0.02
++Trichosuru 5 0.10 0.03
++Phalanger 6 0.12 0.04
++Philander 7 0.08 0.03 8 iterations until convergence
++Bos 8 0.13 0.04 log L: -603.37
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)100:0.05953,
+-((Sarcophilu:0.13180,Dasyurus:0.00572)100:0.08585,(Philander:0.08995,
+-Bos:0.13479)71:0.04220,Echymipera:0.13997)73:0.05457);
++(Thylacinus:0.11,(Trichosuru:0.10,Phalanger:0.12)100:0.05,
++((Sarcophilu:0.13,Dasyurus:0.00)100:0.08,(Philander:0.08,
++Bos:0.13)71:0.04,Echymipera:0.13)73:0.05);
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK)
+@@ -350,30 +350,30 @@ If the automatic search misplaces the ro
+ Tree drawn as unrooted tree for better comparison with non-clock tree!
+
+ branch length nc/c branch length nc/c (= non-clock/clock)
+-Thylacinus 1 0.14706 0.750 9 0.04504 1.322
+-Sarcophilu 2 0.06189 2.130 10 0.06663 1.288
+-Dasyurus 3 0.06189 0.092 11 0.03304 1.277
+-Echymipera 4 0.12852 1.089 12 0.01851 2.948
+-Trichosuru 5 0.10199 1.045
+-Phalanger 6 0.10199 1.202
+-Philander 7 0.09549 0.942 6 iterations until convergence
+-Bos 8 0.09549 1.412 log L: -610.75
++Thylacinus 1 0.14 0.75 9 0.04 1.32
++Sarcophilu 2 0.06 2.13 10 0.06 1.28
++Dasyurus 3 0.06 0.09 11 0.03 1.27
++Echymipera 4 0.12 1.08 12 0.01 2.94
++Trichosuru 5 0.10 1.04
++Phalanger 6 0.10 1.20
++Philander 7 0.09 0.94 6 iterations until convergence
++Bos 8 0.09 1.41 log L: -610.75
+
+ height S.E. of node common to branches
+-0.10199 0.01922 9 5 6
+-0.06189 0.01495 10 2 3
+-0.09549 0.01498 11 7 8
+-0.12852 0.01108 12 10 11 4
+-0.14704 0.01235 1 9 12
+-0.14705 0.02366 of root at branch 1
++0.10 0.01 9 5 6
++0.06 0.01 10 2 3
++0.09 0.01 11 7 8
++0.12 0.01 12 10 11 4
++0.14 0.01 1 9 12
++0.14 0.02 of root at branch 1
+
+
+ Rooted consensus tree with clocklike maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)100:0.04504
+-,((Sarcophilu:0.06189,Dasyurus:0.06189)100:0.06663,(Philander:0.09549,
+-Bos:0.09549)71:0.03304,Echymipera:0.12852)73:0.01851):0.00001);
++(Thylacinus:0.14,((Trichosuru:0.10,Phalanger:0.10)100:0.04
++,((Sarcophilu:0.06,Dasyurus:0.06)100:0.06,(Philander:0.09,
++Bos:0.09)71:0.03,Echymipera:0.12)73:0.01):0.00);
+
+
+ MOLECULAR CLOCK LIKELIHOOD RATIO TEST
+--- a/tests/check-qp-hky-clock-nucl
++++ b/tests/check-qp-hky-clock-nucl
+@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+
+ Rate matrix R (parameters restricted to selected model):
+
+- A-C rate: 1.00000
+- A-G rate: 2.98614
+- A-T rate: 1.00000
+- C-G rate: 1.00000
+- C-T rate: 2.98614
+- G-T rate: 1.00000
++ A-C rate: 1.00
++ A-G rate: 2.98
++ A-T rate: 1.00
++ C-G rate: 1.00
++ C-T rate: 2.98
++ G-T rate: 1.00
+
+ Nucleotide frequencies (estimated from data set):
+
+@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 8
+-Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246
+- 0.23734
+-Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008
+- 0.29786
+-Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801
+- 0.23883
+-Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041
+- 0.27215
+-Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562
+- 0.27148
+-Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036
+- 0.33042
+-Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000
+- 0.22452
+-Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452
+- 0.00000
+-
+-Average distance (over all possible pairs of sequences): 0.25459
+- minimum : 0.13169, maximum : 0.33871
+- variance : 0.00207, std.dev. : 0.04544
++Thylacinus 0.00 0.25 0.22 0.24 0.26 0.24 0.22
++ 0.23
++Sarcophilu 0.25 0.00 0.13 0.26 0.28 0.32 0.26
++ 0.29
++Dasyurus 0.22 0.13 0.00 0.20 0.24 0.25 0.17
++ 0.23
++Echymipera 0.24 0.26 0.20 0.00 0.29 0.33 0.23
++ 0.27
++Trichosuru 0.26 0.28 0.24 0.29 0.00 0.21 0.28
++ 0.27
++Phalanger 0.24 0.32 0.25 0.33 0.21 0.00 0.29
++ 0.33
++Philander 0.22 0.26 0.17 0.23 0.28 0.29 0.00
++ 0.22
++Bos 0.23 0.29 0.23 0.27 0.27 0.33 0.22
++ 0.00
++
++Average distance (over all possible pairs of sequences): 0.25
++ minimum : 0.13, maximum : 0.33
++ variance : 0.00, std.dev. : 0.04
+
+
+ RATE HETEROGENEITY
+@@ -239,40 +239,40 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****..** : 999 (0.999)
+- *..***** : 999 (0.999)
+- *...**.. : 730 (0.730)
+- ******.. : 711 (0.711)
++ ****..** : 999 (0.99)
++ *..***** : 999 (0.99)
++ *...**.. : 730 (0.73)
++ ******.. : 711 (0.71)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *...**** : 466 (0.466)
++ *...**** : 466 (0.46)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ***.**.. : 333 (0.333)
+- *...**.* : 171 (0.171)
+- ***.**.* : 89 (0.089)
+- *..***.. : 80 (0.080)
+- *.....** : 79 (0.079)
+- *..*..** : 69 (0.069)
+- ****..*. : 51 (0.051)
+- *......* : 34 (0.034)
+- *..***.* : 30 (0.030)
+- ****.... : 28 (0.028)
+- ***.***. : 27 (0.027)
+- *..*.... : 22 (0.022)
+- *...***. : 20 (0.020)
+- ***..... : 19 (0.019)
+- *.....*. : 14 (0.014)
+- *..****. : 9 (0.009)
+- *..*..*. : 8 (0.008)
+- ***...** : 6 (0.006)
+- ***....* : 4 (0.004)
+- ****.**. : 1 (0.001)
++ ***.**.. : 333 (0.33)
++ *...**.* : 171 (0.17)
++ ***.**.* : 89 (0.08)
++ *..***.. : 80 (0.08)
++ *.....** : 79 (0.07)
++ *..*..** : 69 (0.06)
++ ****..*. : 51 (0.05)
++ *......* : 34 (0.03)
++ *..***.* : 30 (0.03)
++ ****.... : 28 (0.02)
++ ***.***. : 27 (0.02)
++ *..*.... : 22 (0.02)
++ *...***. : 20 (0.02)
++ ***..... : 19 (0.01)
++ *.....*. : 14 (0.01)
++ *..****. : 9 (0.00)
++ *..*..*. : 8 (0.00)
++ ***...** : 6 (0.00)
++ ***....* : 4 (0.00)
++ ****.**. : 1 (0.00)
+
+ (1 other less frequent bipartitions not shown)
+
+@@ -301,22 +301,22 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382
+-Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452
+-Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513
+-Echymipera 4 0.13997 0.04108 12 0.05457 0.02998
+-Trichosuru 5 0.10654 0.03770
+-Phalanger 6 0.12258 0.04064
+-Philander 7 0.08995 0.03428 8 iterations until convergence
+-Bos 8 0.13479 0.04095 log L: -603.37
++Thylacinus 1 0.11 0.03 9 0.05 0.03
++Sarcophilu 2 0.13 0.03 10 0.08 0.03
++Dasyurus 3 0.00 0.01 11 0.04 0.02
++Echymipera 4 0.13 0.04 12 0.05 0.02
++Trichosuru 5 0.10 0.03
++Phalanger 6 0.12 0.04
++Philander 7 0.08 0.03 8 iterations until convergence
++Bos 8 0.13 0.04 log L: -603.37
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)100:0.05953,
+-((Sarcophilu:0.13180,Dasyurus:0.00572)100:0.08585,(Philander:0.08995,
+-Bos:0.13479)71:0.04220,Echymipera:0.13997)73:0.05457);
++(Thylacinus:0.11,(Trichosuru:0.10,Phalanger:0.12)100:0.05,
++((Sarcophilu:0.13,Dasyurus:0.00)100:0.08,(Philander:0.08,
++Bos:0.13)71:0.04,Echymipera:0.13)73:0.05);
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK)
+@@ -350,30 +350,30 @@ If the automatic search misplaces the ro
+ Tree drawn as unrooted tree for better comparison with non-clock tree!
+
+ branch length nc/c branch length nc/c (= non-clock/clock)
+-Thylacinus 1 0.14706 0.750 9 0.04504 1.322
+-Sarcophilu 2 0.06189 2.130 10 0.06663 1.288
+-Dasyurus 3 0.06189 0.092 11 0.03304 1.277
+-Echymipera 4 0.12852 1.089 12 0.01851 2.948
+-Trichosuru 5 0.10199 1.045
+-Phalanger 6 0.10199 1.202
+-Philander 7 0.09549 0.942 6 iterations until convergence
+-Bos 8 0.09549 1.412 log L: -610.75
++Thylacinus 1 0.14 0.75 9 0.04 1.32
++Sarcophilu 2 0.06 2.13 10 0.06 1.28
++Dasyurus 3 0.06 0.09 11 0.03 1.27
++Echymipera 4 0.12 1.08 12 0.01 2.94
++Trichosuru 5 0.10 1.04
++Phalanger 6 0.10 1.20
++Philander 7 0.09 0.94 6 iterations until convergence
++Bos 8 0.09 1.41 log L: -610.75
+
+ height S.E. of node common to branches
+-0.10199 0.01922 9 5 6
+-0.06189 0.01495 10 2 3
+-0.09549 0.01498 11 7 8
+-0.12852 0.01108 12 10 11 4
+-0.14704 0.01235 1 9 12
+-0.14705 0.02366 of root at branch 1
++0.10 0.01 9 5 6
++0.06 0.01 10 2 3
++0.09 0.01 11 7 8
++0.12 0.01 12 10 11 4
++0.14 0.01 1 9 12
++0.14 0.02 of root at branch 1
+
+
+ Rooted consensus tree with clocklike maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Thylacinus:0.14705,((Trichosuru:0.10199,Phalanger:0.10199)100:0.04504
+-,((Sarcophilu:0.06189,Dasyurus:0.06189)100:0.06663,(Philander:0.09549,
+-Bos:0.09549)71:0.03304,Echymipera:0.12852)73:0.01851):0.00001);
++(Thylacinus:0.14,((Trichosuru:0.10,Phalanger:0.10)100:0.04
++,((Sarcophilu:0.06,Dasyurus:0.06)100:0.06,(Philander:0.09,
++Bos:0.09)71:0.03,Echymipera:0.12)73:0.01):0.00);
+
+
+ MOLECULAR CLOCK LIKELIHOOD RATIO TEST
+--- a/tests/check-qp-hky-rhet-clock-nucl
++++ b/tests/check-qp-hky-rhet-clock-nucl
+@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+
+ Rate matrix R (parameters restricted to selected model):
+
+- A-C rate: 1.00000
+- A-G rate: 4.86122
+- A-T rate: 1.00000
+- C-G rate: 1.00000
+- C-T rate: 4.86122
+- G-T rate: 1.00000
++ A-C rate: 1.00
++ A-G rate: 4.86
++ A-T rate: 1.00
++ C-G rate: 1.00
++ C-T rate: 4.86
++ G-T rate: 1.00
+
+ Nucleotide frequencies (estimated from data set):
+
+@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 8
+-Thylacinus 0.00000 0.43053 0.31881 0.42777 0.48001 0.46047 0.36257
+- 0.45946
+-Sarcophilu 0.43053 0.00000 0.16226 0.50810 0.56683 0.75575 0.50979
+- 0.63867
+-Dasyurus 0.31881 0.16226 0.00000 0.32754 0.43706 0.49686 0.26949
+- 0.46769
+-Echymipera 0.42777 0.50810 0.32754 0.00000 0.56231 0.75320 0.35005
+- 0.54053
+-Trichosuru 0.48001 0.56683 0.43706 0.56231 0.00000 0.32946 0.56635
+- 0.51026
+-Phalanger 0.46047 0.75575 0.49686 0.75320 0.32946 0.00000 0.64553
+- 0.79725
+-Philander 0.36257 0.50979 0.26949 0.35005 0.56635 0.64553 0.00000
+- 0.40838
+-Bos 0.45946 0.63867 0.46769 0.54053 0.51026 0.79725 0.40838
+- 0.00000
+-
+-Average distance (over all possible pairs of sequences): 0.48368
+- minimum : 0.16226, maximum : 0.79725
+- variance : 0.02195, std.dev. : 0.14817
++Thylacinus 0.00 0.43 0.31 0.42 0.48 0.46 0.36
++ 0.45
++Sarcophilu 0.43 0.00 0.16 0.50 0.56 0.75 0.50
++ 0.63
++Dasyurus 0.31 0.16 0.00 0.32 0.43 0.49 0.26
++ 0.46
++Echymipera 0.42 0.50 0.32 0.00 0.56 0.75 0.35
++ 0.54
++Trichosuru 0.48 0.56 0.43 0.56 0.00 0.32 0.56
++ 0.51
++Phalanger 0.46 0.75 0.49 0.75 0.32 0.00 0.64
++ 0.79
++Philander 0.36 0.50 0.26 0.35 0.56 0.64 0.00
++ 0.40
++Bos 0.45 0.63 0.46 0.54 0.51 0.79 0.40
++ 0.00
++
++Average distance (over all possible pairs of sequences): 0.48
++ minimum : 0.16, maximum : 0.79
++ variance : 0.02, std.dev. : 0.14
+
+
+ RATE HETEROGENEITY
+@@ -157,10 +157,10 @@ Number of Gamma rate categories: 4
+ Rates and their respective probabilities used in the likelihood function:
+
+ Category Relative rate Probability
+- 1 0.0007 0.2500
+- 2 0.0674 0.2500
+- 3 0.5911 0.2500
+- 4 3.3407 0.2500
++ 1 0.00 0.25
++ 2 0.06 0.25
++ 3 0.59 0.25
++ 4 3.34 0.25
+
+ Categories 1-4 approximate a continuous Gamma-distribution with expectation 1
+ and variance 3.91.
+@@ -260,40 +260,40 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****..** : 977 (0.977)
+- *..***** : 966 (0.966)
+- *...**.. : 591 (0.591)
++ ****..** : 977 (0.97)
++ *..***** : 966 (0.96)
++ *...**.. : 591 (0.59)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ***.**.* : 289 (0.289)
+- ***.**.. : 257 (0.257)
++ ***.**.* : 289 (0.28)
++ ***.**.. : 257 (0.25)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ******.. : 256 (0.256)
+- ***.***. : 240 (0.240)
+- *...**** : 177 (0.177)
+- *...**.* : 148 (0.148)
+- *..***.* : 130 (0.130)
+- *..***.. : 102 (0.102)
+- *......* : 95 (0.095)
+- *..****. : 92 (0.092)
+- *...***. : 91 (0.091)
+- *..*..** : 82 (0.082)
+- ***..... : 70 (0.070)
+- ****..*. : 69 (0.069)
+- ****.... : 36 (0.036)
+- *..*.... : 36 (0.036)
+- *.....*. : 36 (0.036)
+- *.....** : 32 (0.032)
+- ***....* : 31 (0.031)
+- ***...** : 31 (0.031)
+- *..*...* : 26 (0.026)
+- *..*..*. : 26 (0.026)
++ ******.. : 256 (0.25)
++ ***.***. : 240 (0.24)
++ *...**** : 177 (0.17)
++ *...**.* : 148 (0.14)
++ *..***.* : 130 (0.13)
++ *..***.. : 102 (0.10)
++ *......* : 95 (0.09)
++ *..****. : 92 (0.09)
++ *...***. : 91 (0.09)
++ *..*..** : 82 (0.08)
++ ***..... : 70 (0.07)
++ ****..*. : 69 (0.06)
++ ****.... : 36 (0.03)
++ *..*.... : 36 (0.03)
++ *.....*. : 36 (0.03)
++ *.....** : 32 (0.03)
++ ***....* : 31 (0.03)
++ ***...** : 31 (0.03)
++ *..*...* : 26 (0.02)
++ *..*..*. : 26 (0.02)
+
+ (29 other less frequent bipartitions not shown)
+
+@@ -322,14 +322,14 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-Thylacinus 1 0.13266 0.07077 9 0.14146 0.08889
+-Sarcophilu 2 0.16398 0.05399 10 0.15536 0.07510
+-Dasyurus 3 0.00001 0.00141 11 0.07879 0.07178
+-Echymipera 4 0.20360 0.08378
+-Trichosuru 5 0.15345 0.07805
+-Phalanger 6 0.18858 0.08736
+-Philander 7 0.16082 0.07443 10 iterations until convergence
+-Bos 8 0.30632 0.12025 log L: -569.50
++Thylacinus 1 0.13 0.07 9 0.14 0.08
++Sarcophilu 2 0.16 0.05 10 0.15 0.07
++Dasyurus 3 0.00 0.00 11 0.07 0.07
++Echymipera 4 0.20 0.08
++Trichosuru 5 0.15 0.07
++Phalanger 6 0.18 0.08
++Philander 7 0.16 0.07 10 iterations until convergence
++Bos 8 0.30 0.12 log L: -569.50
+
+ WARNING --- at least one branch length is close to an internal boundary!
+
+@@ -337,9 +337,9 @@ WARNING --- at least one branch length i
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Thylacinus:0.13266,(Trichosuru:0.15345,Phalanger:0.18858)98:0.14146,
+-((Sarcophilu:0.16398,Dasyurus:0.00001)97:0.15536,Echymipera:0.20360,
+-Philander:0.16082,Bos:0.30632)59:0.07879);
++(Thylacinus:0.13,(Trichosuru:0.15,Phalanger:0.18)98:0.14,
++((Sarcophilu:0.16,Dasyurus:0.00)97:0.15,Echymipera:0.20,
++Philander:0.16,Bos:0.30)59:0.07);
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK)
+@@ -373,29 +373,29 @@ If the automatic search misplaces the ro
+ Tree drawn as unrooted tree for better comparison with non-clock tree!
+
+ branch length nc/c branch length nc/c (= non-clock/clock)
+-Thylacinus 1 0.23195 0.572 9 0.16278 0.869
+-Sarcophilu 2 0.07833 2.094 10 0.14771 1.052
+-Dasyurus 3 0.07833 0.000 11 0.00592 13.307
+-Echymipera 4 0.22603 0.901
+-Trichosuru 5 0.17300 0.887
+-Phalanger 6 0.17300 1.090
+-Philander 7 0.22603 0.711 13 iterations until convergence
+-Bos 8 0.22603 1.355 log L: -574.14
++Thylacinus 1 0.23 0.57 9 0.16 0.86
++Sarcophilu 2 0.07 2.09 10 0.14 1.05
++Dasyurus 3 0.07 0.00 11 0.00 13.30
++Echymipera 4 0.22 0.90
++Trichosuru 5 0.17 0.88
++Phalanger 6 0.17 1.09
++Philander 7 0.22 0.71 13 iterations until convergence
++Bos 8 0.22 1.35 log L: -574.14
+
+ height S.E. of node common to branches
+-0.17300 0.05161 9 5 6
+-0.07833 0.02407 10 2 3
+-0.22603 0.03673 11 10 4 7 8
+-0.23195 0.04168 9 11 1
+-0.28387 0.04995 of root at branch 9
++0.17 0.05 9 5 6
++0.07 0.02 10 2 3
++0.22 0.03 11 10 4 7 8
++0.23 0.04 9 11 1
++0.28 0.04 of root at branch 9
+
+
+ Rooted consensus tree with clocklike maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-((Trichosuru:0.17300,Phalanger:0.17300)98:0.11086,(((Sarcophilu:0.07833,
+-Dasyurus:0.07833)97:0.14771,Echymipera:0.22603,Philander:0.22603,
+-Bos:0.22603)59:0.00592,Thylacinus:0.23195):0.05191);
++((Trichosuru:0.17,Phalanger:0.17)98:0.11,(((Sarcophilu:0.07,
++Dasyurus:0.07)97:0.14,Echymipera:0.22,Philander:0.22,
++Bos:0.22)59:0.00,Thylacinus:0.23):0.05);
+
+
+ MOLECULAR CLOCK LIKELIHOOD RATIO TEST
+--- a/tests/check-qp-hky-rhet-nucl
++++ b/tests/check-qp-hky-rhet-nucl
+@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+
+ Rate matrix R (parameters restricted to selected model):
+
+- A-C rate: 1.00000
+- A-G rate: 4.86122
+- A-T rate: 1.00000
+- C-G rate: 1.00000
+- C-T rate: 4.86122
+- G-T rate: 1.00000
++ A-C rate: 1.00
++ A-G rate: 4.86
++ A-T rate: 1.00
++ C-G rate: 1.00
++ C-T rate: 4.86
++ G-T rate: 1.00
+
+ Nucleotide frequencies (estimated from data set):
+
+@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 8
+-Thylacinus 0.00000 0.43053 0.31881 0.42777 0.48001 0.46047 0.36257
+- 0.45946
+-Sarcophilu 0.43053 0.00000 0.16226 0.50810 0.56683 0.75575 0.50979
+- 0.63867
+-Dasyurus 0.31881 0.16226 0.00000 0.32754 0.43706 0.49686 0.26949
+- 0.46769
+-Echymipera 0.42777 0.50810 0.32754 0.00000 0.56231 0.75320 0.35005
+- 0.54053
+-Trichosuru 0.48001 0.56683 0.43706 0.56231 0.00000 0.32946 0.56635
+- 0.51026
+-Phalanger 0.46047 0.75575 0.49686 0.75320 0.32946 0.00000 0.64553
+- 0.79725
+-Philander 0.36257 0.50979 0.26949 0.35005 0.56635 0.64553 0.00000
+- 0.40838
+-Bos 0.45946 0.63867 0.46769 0.54053 0.51026 0.79725 0.40838
+- 0.00000
+-
+-Average distance (over all possible pairs of sequences): 0.48368
+- minimum : 0.16226, maximum : 0.79725
+- variance : 0.02195, std.dev. : 0.14817
++Thylacinus 0.00 0.43 0.31 0.42 0.48 0.46 0.36
++ 0.45
++Sarcophilu 0.43 0.00 0.16 0.50 0.56 0.75 0.50
++ 0.63
++Dasyurus 0.31 0.16 0.00 0.32 0.43 0.49 0.26
++ 0.46
++Echymipera 0.42 0.50 0.32 0.00 0.56 0.75 0.35
++ 0.54
++Trichosuru 0.48 0.56 0.43 0.56 0.00 0.32 0.56
++ 0.51
++Phalanger 0.46 0.75 0.49 0.75 0.32 0.00 0.64
++ 0.79
++Philander 0.36 0.50 0.26 0.35 0.56 0.64 0.00
++ 0.40
++Bos 0.45 0.63 0.46 0.54 0.51 0.79 0.40
++ 0.00
++
++Average distance (over all possible pairs of sequences): 0.48
++ minimum : 0.16, maximum : 0.79
++ variance : 0.02, std.dev. : 0.14
+
+
+ RATE HETEROGENEITY
+@@ -157,10 +157,10 @@ Number of Gamma rate categories: 4
+ Rates and their respective probabilities used in the likelihood function:
+
+ Category Relative rate Probability
+- 1 0.0007 0.2500
+- 2 0.0674 0.2500
+- 3 0.5911 0.2500
+- 4 3.3407 0.2500
++ 1 0.00 0.25
++ 2 0.06 0.25
++ 3 0.59 0.25
++ 4 3.34 0.25
+
+ Categories 1-4 approximate a continuous Gamma-distribution with expectation 1
+ and variance 3.91.
+@@ -260,40 +260,40 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****..** : 977 (0.977)
+- *..***** : 966 (0.966)
+- *...**.. : 591 (0.591)
++ ****..** : 977 (0.97)
++ *..***** : 966 (0.96)
++ *...**.. : 591 (0.59)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ***.**.* : 289 (0.289)
+- ***.**.. : 257 (0.257)
++ ***.**.* : 289 (0.28)
++ ***.**.. : 257 (0.25)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ******.. : 256 (0.256)
+- ***.***. : 240 (0.240)
+- *...**** : 177 (0.177)
+- *...**.* : 148 (0.148)
+- *..***.* : 130 (0.130)
+- *..***.. : 102 (0.102)
+- *......* : 95 (0.095)
+- *..****. : 92 (0.092)
+- *...***. : 91 (0.091)
+- *..*..** : 82 (0.082)
+- ***..... : 70 (0.070)
+- ****..*. : 69 (0.069)
+- ****.... : 36 (0.036)
+- *..*.... : 36 (0.036)
+- *.....*. : 36 (0.036)
+- *.....** : 32 (0.032)
+- ***....* : 31 (0.031)
+- ***...** : 31 (0.031)
+- *..*...* : 26 (0.026)
+- *..*..*. : 26 (0.026)
++ ******.. : 256 (0.25)
++ ***.***. : 240 (0.24)
++ *...**** : 177 (0.17)
++ *...**.* : 148 (0.14)
++ *..***.* : 130 (0.13)
++ *..***.. : 102 (0.10)
++ *......* : 95 (0.09)
++ *..****. : 92 (0.09)
++ *...***. : 91 (0.09)
++ *..*..** : 82 (0.08)
++ ***..... : 70 (0.07)
++ ****..*. : 69 (0.06)
++ ****.... : 36 (0.03)
++ *..*.... : 36 (0.03)
++ *.....*. : 36 (0.03)
++ *.....** : 32 (0.03)
++ ***....* : 31 (0.03)
++ ***...** : 31 (0.03)
++ *..*...* : 26 (0.02)
++ *..*..*. : 26 (0.02)
+
+ (29 other less frequent bipartitions not shown)
+
+@@ -322,14 +322,14 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-Thylacinus 1 0.13266 0.07077 9 0.14146 0.08889
+-Sarcophilu 2 0.16398 0.05399 10 0.15536 0.07510
+-Dasyurus 3 0.00001 0.00141 11 0.07879 0.07178
+-Echymipera 4 0.20360 0.08378
+-Trichosuru 5 0.15345 0.07805
+-Phalanger 6 0.18858 0.08736
+-Philander 7 0.16082 0.07443 10 iterations until convergence
+-Bos 8 0.30632 0.12025 log L: -569.50
++Thylacinus 1 0.13 0.07 9 0.14 0.08
++Sarcophilu 2 0.16 0.05 10 0.15 0.07
++Dasyurus 3 0.00 0.00 11 0.07 0.07
++Echymipera 4 0.20 0.08
++Trichosuru 5 0.15 0.07
++Phalanger 6 0.18 0.08
++Philander 7 0.16 0.07 10 iterations until convergence
++Bos 8 0.30 0.12 log L: -569.50
+
+ WARNING --- at least one branch length is close to an internal boundary!
+
+@@ -337,9 +337,9 @@ WARNING --- at least one branch length i
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Thylacinus:0.13266,(Trichosuru:0.15345,Phalanger:0.18858)98:0.14146,
+-((Sarcophilu:0.16398,Dasyurus:0.00001)97:0.15536,Echymipera:0.20360,
+-Philander:0.16082,Bos:0.30632)59:0.07879);
++(Thylacinus:0.13,(Trichosuru:0.15,Phalanger:0.18)98:0.14,
++((Sarcophilu:0.16,Dasyurus:0.00)97:0.15,Echymipera:0.20,
++Philander:0.16,Bos:0.30)59:0.07);
+
+
+ TIME STAMP
+--- a/tests/check-qp-jtt-prot
++++ b/tests/check-qp-jtt-prot
+@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.17343 0.93732 0.96340 2.06393 1.74159 2.60857
+-HBB_HORSE 0.17343 0.00000 0.97297 0.97742 2.03298 1.75271 2.65715
+-HBA_HUMAN 0.93732 0.97297 0.00000 0.12200 1.93956 1.25126 2.51688
+-HBA_HORSE 0.96340 0.97742 0.12200 0.00000 1.99570 1.34817 2.47562
+-MYG_PHYCA 2.06393 2.03298 1.93956 1.99570 0.00000 2.04426 2.69086
+-GLB5_PETMA 1.74159 1.75271 1.25126 1.34817 2.04426 0.00000 2.23399
+-LGB2_LUPLU 2.60857 2.65715 2.51688 2.47562 2.69086 2.23399 0.00000
+-
+-Average distance (over all possible pairs of sequences): 1.69047
+- minimum : 0.12200, maximum : 2.69086
+- variance : 0.60537, std.dev. : 0.77805
++HBB_HUMAN 0.00 0.17 0.93 0.96 2.06 1.74 2.60
++HBB_HORSE 0.17 0.00 0.97 0.97 2.03 1.75 2.65
++HBA_HUMAN 0.93 0.97 0.00 0.12 1.93 1.25 2.51
++HBA_HORSE 0.96 0.97 0.12 0.00 1.99 1.34 2.47
++MYG_PHYCA 2.06 2.03 1.93 1.99 0.00 2.04 2.69
++GLB5_PETMA 1.74 1.75 1.25 1.34 2.04 0.00 2.23
++LGB2_LUPLU 2.60 2.65 2.51 2.47 2.69 2.23 0.00
++
++Average distance (over all possible pairs of sequences): 1.69
++ minimum : 0.12, maximum : 2.69
++ variance : 0.60, std.dev. : 0.77
+
+
+ RATE HETEROGENEITY
+@@ -229,21 +229,21 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- **..*** : 1000 (1.000)
+- ****... : 1000 (1.000)
+- **..... : 1000 (1.000)
++ **..*** : 1000 (1.00)
++ ****... : 1000 (1.00)
++ **..... : 1000 (1.00)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *****.. : 480 (0.480)
++ *****.. : 480 (0.48)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****.*. : 447 (0.447)
+- ****..* : 73 (0.073)
++ ****.*. : 447 (0.44)
++ ****..* : 73 (0.07)
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
+@@ -268,21 +268,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04638 0.03177 8 0.25373 0.08572
+-HBB_HORSE 2 0.12734 0.03889 9 0.42250 0.12721
+-HBA_HUMAN 3 0.02556 0.02189 10 0.61836 0.11268
+-HBA_HORSE 4 0.09596 0.03156
+-MYG_PHYCA 5 1.31229 0.21005
+-GLB5_PETMA 6 0.68477 0.13677 12 iterations until convergence
+-LGB2_LUPLU 7 1.72937 0.26616 log L: -1707.74
++HBB_HUMAN 1 0.04 0.03 8 0.25 0.08
++HBB_HORSE 2 0.12 0.03 9 0.42 0.12
++HBA_HUMAN 3 0.02 0.02 10 0.61 0.11
++HBA_HORSE 4 0.09 0.03
++MYG_PHYCA 5 1.31 0.21
++GLB5_PETMA 6 0.68 0.13 12 iterations until convergence
++LGB2_LUPLU 7 1.72 0.26 log L: -1707.74
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04638,((HBA_HUMAN:0.02556,HBA_HORSE:0.09596)100:0.25373,
+-(MYG_PHYCA:1.31229,GLB5_PETMA:0.68477,LGB2_LUPLU:1.72937)100:0.42250)
+-100:0.61836,HBB_HORSE:0.12734);
++(HBB_HUMAN:0.04,((HBA_HUMAN:0.02,HBA_HORSE:0.09)100:0.25,
++(MYG_PHYCA:1.31,GLB5_PETMA:0.68,LGB2_LUPLU:1.72)100:0.42)
++100:0.61,HBB_HORSE:0.12);
+
+
+ TIME STAMP
+--- a/tests/check-qp-jtt-rhet-clock-prot
++++ b/tests/check-qp-jtt-rhet-clock-prot
+@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.17871 1.04599 1.08300 2.51519 2.11125 3.24687
+-HBB_HORSE 0.17871 0.00000 1.09480 1.10580 2.48701 2.13026 3.32934
+-HBA_HUMAN 1.04599 1.09480 0.00000 0.12529 2.35552 1.45323 3.25521
+-HBA_HORSE 1.08300 1.10580 0.12529 0.00000 2.43439 1.57394 3.14696
+-MYG_PHYCA 2.51519 2.48701 2.35552 2.43439 0.00000 2.53740 3.41680
+-GLB5_PETMA 2.11125 2.13026 1.45323 1.57394 2.53740 0.00000 2.84462
+-LGB2_LUPLU 3.24687 3.32934 3.25521 3.14696 3.41680 2.84462 0.00000
+-
+-Average distance (over all possible pairs of sequences): 2.07008
+- minimum : 0.12529, maximum : 3.41680
+- variance : 1.03242, std.dev. : 1.01608
++HBB_HUMAN 0.00 0.17 1.04 1.08 2.51 2.11 3.24
++HBB_HORSE 0.17 0.00 1.09 1.10 2.48 2.13 3.32
++HBA_HUMAN 1.04 1.09 0.00 0.12 2.35 1.45 3.25
++HBA_HORSE 1.08 1.10 0.12 0.00 2.43 1.57 3.14
++MYG_PHYCA 2.51 2.48 2.35 2.43 0.00 2.53 3.41
++GLB5_PETMA 2.11 2.13 1.45 1.57 2.53 0.00 2.84
++LGB2_LUPLU 3.24 3.32 3.25 3.14 3.41 2.84 0.00
++
++Average distance (over all possible pairs of sequences): 2.07
++ minimum : 0.12, maximum : 3.41
++ variance : 1.03, std.dev. : 1.01
+
+
+ RATE HETEROGENEITY
+@@ -150,10 +150,10 @@ Number of Gamma rate categories: 4
+ Rates and their respective probabilities used in the likelihood function:
+
+ Category Relative rate Probability
+- 1 0.3690 0.2500
+- 2 0.7199 0.2500
+- 3 1.1100 0.2500
+- 4 1.8010 0.2500
++ 1 0.36 0.25
++ 2 0.71 0.25
++ 3 1.11 0.25
++ 4 1.80 0.25
+
+ Categories 1-4 approximate a continuous Gamma-distribution with expectation 1
+ and variance 0.40.
+@@ -251,21 +251,21 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- **..*** : 1000 (1.000)
+- ****... : 1000 (1.000)
+- **..... : 1000 (1.000)
++ **..*** : 1000 (1.00)
++ ****... : 1000 (1.00)
++ **..... : 1000 (1.00)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *****.. : 480 (0.480)
++ *****.. : 480 (0.48)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****.*. : 447 (0.447)
+- ****..* : 73 (0.073)
++ ****.*. : 447 (0.44)
++ ****..* : 73 (0.07)
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
+@@ -290,21 +290,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04960 0.03397 8 0.23079 0.10535
+-HBB_HORSE 2 0.12883 0.04077 9 0.50896 0.17274
+-HBA_HUMAN 3 0.01975 0.02294 10 0.74671 0.14184
+-HBA_HORSE 4 0.10545 0.03361
+-MYG_PHYCA 5 1.67907 0.30134
+-GLB5_PETMA 6 0.80699 0.18542 11 iterations until convergence
+-LGB2_LUPLU 7 2.33192 0.42328 log L: -1701.58
++HBB_HUMAN 1 0.04 0.03 8 0.23 0.10
++HBB_HORSE 2 0.12 0.04 9 0.50 0.17
++HBA_HUMAN 3 0.01 0.02 10 0.74 0.14
++HBA_HORSE 4 0.10 0.03
++MYG_PHYCA 5 1.67 0.30
++GLB5_PETMA 6 0.80 0.18 11 iterations until convergence
++LGB2_LUPLU 7 2.33 0.42 log L: -1701.58
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04960,((HBA_HUMAN:0.01975,HBA_HORSE:0.10545)100:0.23079,
+-(MYG_PHYCA:1.67907,GLB5_PETMA:0.80699,LGB2_LUPLU:2.33192)100:0.50896)
+-100:0.74671,HBB_HORSE:0.12883);
++(HBB_HUMAN:0.04,((HBA_HUMAN:0.01,HBA_HORSE:0.10)100:0.23,
++(MYG_PHYCA:1.67,GLB5_PETMA:0.80,LGB2_LUPLU:2.33)100:0.50)
++100:0.74,HBB_HORSE:0.12);
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS OF CONSENSUS TREE (WITH CLOCK)
+@@ -336,28 +336,28 @@ If the automatic search misplaces the ro
+ Tree drawn as unrooted tree for better comparison with non-clock tree!
+
+ branch length nc/c branch length nc/c (= non-clock/clock)
+-HBB_HUMAN 1 0.08750 0.567 8 0.51287 0.450
+-HBB_HORSE 2 0.08750 1.472 9 0.57972 0.878
+-HBA_HUMAN 3 0.06482 0.305 10 0.49019 1.523
+-HBA_HORSE 4 0.06482 1.627
+-MYG_PHYCA 5 1.15741 1.451
+-GLB5_PETMA 6 1.15741 0.697 7 iterations until convergence
+-LGB2_LUPLU 7 2.28390 1.021 log L: -1708.22
++HBB_HUMAN 1 0.08 0.56 8 0.51 0.45
++HBB_HORSE 2 0.08 1.47 9 0.57 0.87
++HBA_HUMAN 3 0.06 0.30 10 0.49 1.52
++HBA_HORSE 4 0.06 1.62
++MYG_PHYCA 5 1.15 1.45
++GLB5_PETMA 6 1.15 0.69 7 iterations until convergence
++LGB2_LUPLU 7 2.28 1.02 log L: -1708.22
+
+ height S.E. of node common to branches
+-0.08750 0.02034 10 2 1
+-0.06482 0.01758 8 3 4
+-0.57769 0.07382 9 10 8
+-1.15741 0.11326 7 9 5 6
+-1.72066 0.21547 of root at branch 7
++0.08 0.02 10 2 1
++0.06 0.01 8 3 4
++0.57 0.07 9 10 8
++1.15 0.11 7 9 5 6
++1.72 0.21 of root at branch 7
+
+
+ Rooted consensus tree with clocklike maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(LGB2_LUPLU:1.72066,(((HBB_HORSE:0.08750,HBB_HUMAN:0.08750):0.49019
+-,(HBA_HUMAN:0.06482,HBA_HORSE:0.06482)100:0.51287):0.57972,MYG_PHYCA:1.15741,
+-GLB5_PETMA:1.15741):0.56324);
++(LGB2_LUPLU:1.72,(((HBB_HORSE:0.08,HBB_HUMAN:0.08):0.49
++,(HBA_HUMAN:0.06,HBA_HORSE:0.06)100:0.51):0.57,MYG_PHYCA:1.15,
++GLB5_PETMA:1.15):0.56);
+
+
+ MOLECULAR CLOCK LIKELIHOOD RATIO TEST
+--- a/tests/check-qp-jtt-rhet-prot
++++ b/tests/check-qp-jtt-rhet-prot
+@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.17871 1.04599 1.08300 2.51519 2.11125 3.24687
+-HBB_HORSE 0.17871 0.00000 1.09480 1.10580 2.48701 2.13026 3.32934
+-HBA_HUMAN 1.04599 1.09480 0.00000 0.12529 2.35552 1.45323 3.25521
+-HBA_HORSE 1.08300 1.10580 0.12529 0.00000 2.43439 1.57394 3.14696
+-MYG_PHYCA 2.51519 2.48701 2.35552 2.43439 0.00000 2.53740 3.41680
+-GLB5_PETMA 2.11125 2.13026 1.45323 1.57394 2.53740 0.00000 2.84462
+-LGB2_LUPLU 3.24687 3.32934 3.25521 3.14696 3.41680 2.84462 0.00000
+-
+-Average distance (over all possible pairs of sequences): 2.07008
+- minimum : 0.12529, maximum : 3.41680
+- variance : 1.03242, std.dev. : 1.01608
++HBB_HUMAN 0.00 0.17 1.04 1.08 2.51 2.11 3.24
++HBB_HORSE 0.17 0.00 1.09 1.10 2.48 2.13 3.32
++HBA_HUMAN 1.04 1.09 0.00 0.12 2.35 1.45 3.25
++HBA_HORSE 1.08 1.10 0.12 0.00 2.43 1.57 3.14
++MYG_PHYCA 2.51 2.48 2.35 2.43 0.00 2.53 3.41
++GLB5_PETMA 2.11 2.13 1.45 1.57 2.53 0.00 2.84
++LGB2_LUPLU 3.24 3.32 3.25 3.14 3.41 2.84 0.00
++
++Average distance (over all possible pairs of sequences): 2.07
++ minimum : 0.12, maximum : 3.41
++ variance : 1.03, std.dev. : 1.01
+
+
+ RATE HETEROGENEITY
+@@ -150,10 +150,10 @@ Number of Gamma rate categories: 4
+ Rates and their respective probabilities used in the likelihood function:
+
+ Category Relative rate Probability
+- 1 0.3690 0.2500
+- 2 0.7199 0.2500
+- 3 1.1100 0.2500
+- 4 1.8010 0.2500
++ 1 0.36 0.25
++ 2 0.71 0.25
++ 3 1.11 0.25
++ 4 1.80 0.25
+
+ Categories 1-4 approximate a continuous Gamma-distribution with expectation 1
+ and variance 0.40.
+@@ -251,21 +251,21 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- **..*** : 1000 (1.000)
+- ****... : 1000 (1.000)
+- **..... : 1000 (1.000)
++ **..*** : 1000 (1.00)
++ ****... : 1000 (1.00)
++ **..... : 1000 (1.00)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *****.. : 480 (0.480)
++ *****.. : 480 (0.48)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****.*. : 447 (0.447)
+- ****..* : 73 (0.073)
++ ****.*. : 447 (0.44)
++ ****..* : 73 (0.07)
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
+@@ -290,21 +290,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04960 0.03397 8 0.23079 0.10535
+-HBB_HORSE 2 0.12883 0.04077 9 0.50896 0.17274
+-HBA_HUMAN 3 0.01975 0.02294 10 0.74671 0.14184
+-HBA_HORSE 4 0.10545 0.03361
+-MYG_PHYCA 5 1.67907 0.30134
+-GLB5_PETMA 6 0.80699 0.18542 11 iterations until convergence
+-LGB2_LUPLU 7 2.33192 0.42328 log L: -1701.58
++HBB_HUMAN 1 0.04 0.03 8 0.23 0.10
++HBB_HORSE 2 0.12 0.04 9 0.50 0.17
++HBA_HUMAN 3 0.01 0.02 10 0.74 0.14
++HBA_HORSE 4 0.10 0.03
++MYG_PHYCA 5 1.67 0.30
++GLB5_PETMA 6 0.80 0.18 11 iterations until convergence
++LGB2_LUPLU 7 2.33 0.42 log L: -1701.58
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04960,((HBA_HUMAN:0.01975,HBA_HORSE:0.10545)100:0.23079,
+-(MYG_PHYCA:1.67907,GLB5_PETMA:0.80699,LGB2_LUPLU:2.33192)100:0.50896)
+-100:0.74671,HBB_HORSE:0.12883);
++(HBB_HUMAN:0.04,((HBA_HUMAN:0.01,HBA_HORSE:0.10)100:0.23,
++(MYG_PHYCA:1.67,GLB5_PETMA:0.80,LGB2_LUPLU:2.33)100:0.50)
++100:0.74,HBB_HORSE:0.12);
+
+
+ TIME STAMP
+--- a/tests/check-qp-mtrev-prot
++++ b/tests/check-qp-mtrev-prot
+@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.19615 1.12348 1.16856 2.59690 2.15305 3.47989
+-HBB_HORSE 0.19615 0.00000 1.17857 1.20524 2.74793 2.18071 3.63316
+-HBA_HUMAN 1.12348 1.17857 0.00000 0.13144 2.41361 1.43785 3.06000
+-HBA_HORSE 1.16856 1.20524 0.13144 0.00000 2.44163 1.55582 3.05140
+-MYG_PHYCA 2.59690 2.74793 2.41361 2.44163 0.00000 2.62256 3.47779
+-GLB5_PETMA 2.15305 2.18071 1.43785 1.55582 2.62256 0.00000 2.97722
+-LGB2_LUPLU 3.47989 3.63316 3.06000 3.05140 3.47779 2.97722 0.00000
+-
+-Average distance (over all possible pairs of sequences): 2.13490
+- minimum : 0.13144, maximum : 3.63316
+- variance : 1.07966, std.dev. : 1.03906
++HBB_HUMAN 0.00 0.19 1.12 1.16 2.59 2.15 3.47
++HBB_HORSE 0.19 0.00 1.17 1.20 2.74 2.18 3.63
++HBA_HUMAN 1.12 1.17 0.00 0.13 2.41 1.43 3.06
++HBA_HORSE 1.16 1.20 0.13 0.00 2.44 1.55 3.05
++MYG_PHYCA 2.59 2.74 2.41 2.44 0.00 2.62 3.47
++GLB5_PETMA 2.15 2.18 1.43 1.55 2.62 0.00 2.97
++LGB2_LUPLU 3.47 3.63 3.06 3.05 3.47 2.97 0.00
++
++Average distance (over all possible pairs of sequences): 2.13
++ minimum : 0.13, maximum : 3.63
++ variance : 1.07, std.dev. : 1.03
+
+
+ RATE HETEROGENEITY
+@@ -229,24 +229,24 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- **..*** : 1000 (1.000)
+- **..... : 1000 (1.000)
+- ****... : 957 (0.957)
++ **..*** : 1000 (1.00)
++ **..... : 1000 (1.00)
++ ****... : 957 (0.95)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *****.. : 492 (0.492)
++ *****.. : 492 (0.49)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****.*. : 476 (0.476)
+- ****..* : 31 (0.031)
+- **..*.* : 24 (0.024)
+- **..*.. : 19 (0.019)
+- **....* : 1 (0.001)
++ ****.*. : 476 (0.47)
++ ****..* : 31 (0.03)
++ **..*.* : 24 (0.02)
++ **..*.. : 19 (0.01)
++ **....* : 1 (0.00)
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
+@@ -271,21 +271,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.03472 0.03059 8 0.30126 0.09575
+-HBB_HORSE 2 0.16246 0.04359 9 0.34149 0.13763
+-HBA_HUMAN 3 0.04636 0.02527 10 0.70896 0.13056
+-HBA_HORSE 4 0.08355 0.03082
+-MYG_PHYCA 5 1.58550 0.26736
+-GLB5_PETMA 6 0.88663 0.17157 10 iterations until convergence
+-LGB2_LUPLU 7 2.13259 0.35215 log L: -1736.55
++HBB_HUMAN 1 0.03 0.03 8 0.30 0.09
++HBB_HORSE 2 0.16 0.04 9 0.34 0.13
++HBA_HUMAN 3 0.04 0.02 10 0.70 0.13
++HBA_HORSE 4 0.08 0.03
++MYG_PHYCA 5 1.58 0.26
++GLB5_PETMA 6 0.88 0.17 10 iterations until convergence
++LGB2_LUPLU 7 2.13 0.35 log L: -1736.55
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.03472,((HBA_HUMAN:0.04636,HBA_HORSE:0.08355)100:0.30126,
+-(MYG_PHYCA:1.58550,GLB5_PETMA:0.88663,LGB2_LUPLU:2.13259)96:0.34149)
+-100:0.70896,HBB_HORSE:0.16246);
++(HBB_HUMAN:0.03,((HBA_HUMAN:0.04,HBA_HORSE:0.08)100:0.30,
++(MYG_PHYCA:1.58,GLB5_PETMA:0.88,LGB2_LUPLU:2.13)96:0.34)
++100:0.70,HBB_HORSE:0.16);
+
+
+ TIME STAMP
+--- a/tests/check-qp-pure-bin
++++ b/tests/check-qp-pure-bin
+@@ -101,15 +101,15 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 5
+-Gibbon 0.00000 0.05300 0.05176 0.05295 0.06171
+-Human 0.05300 0.00000 0.00563 0.00903 0.04081
+-Chimpanzee 0.05176 0.00563 0.00000 0.01018 0.03960
+-Gorilla 0.05295 0.00903 0.01018 0.00000 0.03835
+-Orangutan 0.06171 0.04081 0.03960 0.03835 0.00000
+-
+-Average distance (over all possible pairs of sequences): 0.03630
+- minimum : 0.00563, maximum : 0.06171
+- variance : 0.00043, std.dev. : 0.02066
++Gibbon 0.00 0.05 0.05 0.05 0.06
++Human 0.05 0.00 0.00 0.00 0.04
++Chimpanzee 0.05 0.00 0.00 0.01 0.03
++Gorilla 0.05 0.00 0.01 0.00 0.03
++Orangutan 0.06 0.04 0.03 0.03 0.00
++
++Average distance (over all possible pairs of sequences): 0.03
++ minimum : 0.00, maximum : 0.06
++ variance : 0.00, std.dev. : 0.02
+
+
+ RATE HETEROGENEITY
+@@ -193,8 +193,8 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *..** : 1000 (1.000)
+- *...* : 1000 (1.000)
++ *..** : 1000 (1.00)
++ *...* : 1000 (1.00)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+@@ -221,18 +221,18 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-Gibbon 1 0.03803 0.00691 6 0.00339 0.00199
+-Human 2 0.00240 0.00170 7 0.01106 0.00384
+-Chimpanzee 3 0.00323 0.00196
+-Gorilla 4 0.00353 0.00206 5 iterations until convergence
+-Orangutan 5 0.02357 0.00543 log L: -968.78
++Gibbon 1 0.03 0.00 6 0.00 0.00
++Human 2 0.00 0.00 7 0.01 0.00
++Chimpanzee 3 0.00 0.00
++Gorilla 4 0.00 0.00 5 iterations until convergence
++Orangutan 5 0.02 0.00 log L: -968.78
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Gibbon:0.03803,((Human:0.00240,Chimpanzee:0.00323)100:0.00339,Gorilla:0.00353)
+-100:0.01106,Orangutan:0.02357);
++(Gibbon:0.03,((Human:0.00,Chimpanzee:0.00)100:0.00,Gorilla:0.00)
++100:0.01,Orangutan:0.02);
+
+
+ TIME STAMP
+--- a/tests/check-qp-pure-nucl
++++ b/tests/check-qp-pure-nucl
+@@ -52,12 +52,12 @@ Transition/transversion parameter (estim
+
+ Rate matrix R (parameters restricted to selected model):
+
+- A-C rate: 1.00000
+- A-G rate: 2.98614
+- A-T rate: 1.00000
+- C-G rate: 1.00000
+- C-T rate: 2.98614
+- G-T rate: 1.00000
++ A-C rate: 1.00
++ A-G rate: 2.98
++ A-T rate: 1.00
++ C-G rate: 1.00
++ C-T rate: 2.98
++ G-T rate: 1.00
+
+ Nucleotide frequencies (estimated from data set):
+
+@@ -126,26 +126,26 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 8
+-Thylacinus 0.00000 0.25562 0.22032 0.24509 0.26007 0.24938 0.22246
+- 0.23734
+-Sarcophilu 0.25562 0.00000 0.13169 0.26969 0.28414 0.32680 0.26008
+- 0.29786
+-Dasyurus 0.22032 0.13169 0.00000 0.20032 0.24821 0.25234 0.17801
+- 0.23883
+-Echymipera 0.24509 0.26969 0.20032 0.00000 0.29531 0.33871 0.23041
+- 0.27215
+-Trichosuru 0.26007 0.28414 0.24821 0.29531 0.00000 0.21136 0.28562
+- 0.27148
+-Phalanger 0.24938 0.32680 0.25234 0.33871 0.21136 0.00000 0.29036
+- 0.33042
+-Philander 0.22246 0.26008 0.17801 0.23041 0.28562 0.29036 0.00000
+- 0.22452
+-Bos 0.23734 0.29786 0.23883 0.27215 0.27148 0.33042 0.22452
+- 0.00000
+-
+-Average distance (over all possible pairs of sequences): 0.25459
+- minimum : 0.13169, maximum : 0.33871
+- variance : 0.00207, std.dev. : 0.04544
++Thylacinus 0.00 0.25 0.22 0.24 0.26 0.24 0.22
++ 0.23
++Sarcophilu 0.25 0.00 0.13 0.26 0.28 0.32 0.26
++ 0.29
++Dasyurus 0.22 0.13 0.00 0.20 0.24 0.25 0.17
++ 0.23
++Echymipera 0.24 0.26 0.20 0.00 0.29 0.33 0.23
++ 0.27
++Trichosuru 0.26 0.28 0.24 0.29 0.00 0.21 0.28
++ 0.27
++Phalanger 0.24 0.32 0.25 0.33 0.21 0.00 0.29
++ 0.33
++Philander 0.22 0.26 0.17 0.23 0.28 0.29 0.00
++ 0.22
++Bos 0.23 0.29 0.23 0.27 0.27 0.33 0.22
++ 0.00
++
++Average distance (over all possible pairs of sequences): 0.25
++ minimum : 0.13, maximum : 0.33
++ variance : 0.00, std.dev. : 0.04
+
+
+ RATE HETEROGENEITY
+@@ -239,40 +239,40 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****..** : 999 (0.999)
+- *..***** : 999 (0.999)
+- *...**.. : 730 (0.730)
+- ******.. : 711 (0.711)
++ ****..** : 999 (0.99)
++ *..***** : 999 (0.99)
++ *...**.. : 730 (0.73)
++ ******.. : 711 (0.71)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *...**** : 466 (0.466)
++ *...**** : 466 (0.46)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ***.**.. : 333 (0.333)
+- *...**.* : 171 (0.171)
+- ***.**.* : 89 (0.089)
+- *..***.. : 80 (0.080)
+- *.....** : 79 (0.079)
+- *..*..** : 69 (0.069)
+- ****..*. : 51 (0.051)
+- *......* : 34 (0.034)
+- *..***.* : 30 (0.030)
+- ****.... : 28 (0.028)
+- ***.***. : 27 (0.027)
+- *..*.... : 22 (0.022)
+- *...***. : 20 (0.020)
+- ***..... : 19 (0.019)
+- *.....*. : 14 (0.014)
+- *..****. : 9 (0.009)
+- *..*..*. : 8 (0.008)
+- ***...** : 6 (0.006)
+- ***....* : 4 (0.004)
+- ****.**. : 1 (0.001)
++ ***.**.. : 333 (0.33)
++ *...**.* : 171 (0.17)
++ ***.**.* : 89 (0.08)
++ *..***.. : 80 (0.08)
++ *.....** : 79 (0.07)
++ *..*..** : 69 (0.06)
++ ****..*. : 51 (0.05)
++ *......* : 34 (0.03)
++ *..***.* : 30 (0.03)
++ ****.... : 28 (0.02)
++ ***.***. : 27 (0.02)
++ *..*.... : 22 (0.02)
++ *...***. : 20 (0.02)
++ ***..... : 19 (0.01)
++ *.....*. : 14 (0.01)
++ *..****. : 9 (0.00)
++ *..*..*. : 8 (0.00)
++ ***...** : 6 (0.00)
++ ***....* : 4 (0.00)
++ ****.**. : 1 (0.00)
+
+ (1 other less frequent bipartitions not shown)
+
+@@ -301,22 +301,22 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-Thylacinus 1 0.11024 0.03812 9 0.05953 0.03382
+-Sarcophilu 2 0.13180 0.03734 10 0.08585 0.03452
+-Dasyurus 3 0.00572 0.01273 11 0.04220 0.02513
+-Echymipera 4 0.13997 0.04108 12 0.05457 0.02998
+-Trichosuru 5 0.10654 0.03770
+-Phalanger 6 0.12258 0.04064
+-Philander 7 0.08995 0.03428 8 iterations until convergence
+-Bos 8 0.13479 0.04095 log L: -603.37
++Thylacinus 1 0.11 0.03 9 0.05 0.03
++Sarcophilu 2 0.13 0.03 10 0.08 0.03
++Dasyurus 3 0.00 0.01 11 0.04 0.02
++Echymipera 4 0.13 0.04 12 0.05 0.02
++Trichosuru 5 0.10 0.03
++Phalanger 6 0.12 0.04
++Philander 7 0.08 0.03 8 iterations until convergence
++Bos 8 0.13 0.04 log L: -603.37
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Thylacinus:0.11024,(Trichosuru:0.10654,Phalanger:0.12258)100:0.05953,
+-((Sarcophilu:0.13180,Dasyurus:0.00572)100:0.08585,(Philander:0.08995,
+-Bos:0.13479)71:0.04220,Echymipera:0.13997)73:0.05457);
++(Thylacinus:0.11,(Trichosuru:0.10,Phalanger:0.12)100:0.05,
++((Sarcophilu:0.13,Dasyurus:0.00)100:0.08,(Philander:0.08,
++Bos:0.13)71:0.04,Echymipera:0.13)73:0.05);
+
+
+ TIME STAMP
+--- a/tests/check-qp-pure-prot
++++ b/tests/check-qp-pure-prot
+@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644
+-HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187
+-HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730
+-HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172
+-MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386
+-GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272
+-LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000
+-
+-Average distance (over all possible pairs of sequences): 1.73823
+- minimum : 0.12147, maximum : 2.86187
+- variance : 0.65214, std.dev. : 0.80755
++HBB_HUMAN 0.00 0.17 0.96 0.99 2.12 1.77 2.78
++HBB_HORSE 0.17 0.00 1.01 1.02 2.09 1.78 2.86
++HBA_HUMAN 0.96 1.01 0.00 0.12 1.93 1.30 2.54
++HBA_HORSE 0.99 1.02 0.12 0.00 2.00 1.39 2.51
++MYG_PHYCA 2.12 2.09 1.93 2.00 0.00 2.12 2.79
++GLB5_PETMA 1.77 1.78 1.30 1.39 2.12 0.00 2.18
++LGB2_LUPLU 2.78 2.86 2.54 2.51 2.79 2.18 0.00
++
++Average distance (over all possible pairs of sequences): 1.73
++ minimum : 0.12, maximum : 2.86
++ variance : 0.65, std.dev. : 0.80
+
+
+ RATE HETEROGENEITY
+@@ -229,10 +229,10 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- **..*** : 1000 (1.000)
+- ****... : 1000 (1.000)
+- **..... : 1000 (1.000)
+- *****.. : 821 (0.821)
++ **..*** : 1000 (1.00)
++ ****... : 1000 (1.00)
++ **..... : 1000 (1.00)
++ *****.. : 821 (0.82)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+@@ -243,8 +243,8 @@ the consensus tree:
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****..* : 105 (0.105)
+- ****.*. : 74 (0.074)
++ ****..* : 105 (0.10)
++ ****.*. : 74 (0.07)
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
+@@ -269,21 +269,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04915 0.03158 8 0.28345 0.08777
+-HBB_HORSE 2 0.12603 0.03871 9 0.18154 0.13086
+-HBA_HUMAN 3 0.02555 0.02185 10 0.34694 0.12552
+-HBA_HORSE 4 0.09542 0.03153 11 0.60239 0.11261
+-MYG_PHYCA 5 1.33166 0.21117
+-GLB5_PETMA 6 0.57466 0.13843 10 iterations until convergence
+-LGB2_LUPLU 7 1.71333 0.27645 log L: -1699.00
++HBB_HUMAN 1 0.04 0.03 8 0.28 0.08
++HBB_HORSE 2 0.12 0.03 9 0.18 0.13
++HBA_HUMAN 3 0.02 0.02 10 0.34 0.12
++HBA_HORSE 4 0.09 0.03 11 0.60 0.11
++MYG_PHYCA 5 1.33 0.21
++GLB5_PETMA 6 0.57 0.13 10 iterations until convergence
++LGB2_LUPLU 7 1.71 0.27 log L: -1699.00
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04915,((HBA_HUMAN:0.02555,HBA_HORSE:0.09542)100:0.28345,
+-((GLB5_PETMA:0.57466,LGB2_LUPLU:1.71333)82:0.18154,MYG_PHYCA:1.33166)
+-100:0.34694)100:0.60239,HBB_HORSE:0.12603);
++(HBB_HUMAN:0.04,((HBA_HUMAN:0.02,HBA_HORSE:0.09)100:0.28,
++((GLB5_PETMA:0.57,LGB2_LUPLU:1.71)82:0.18,MYG_PHYCA:1.33)
++100:0.34)100:0.60,HBB_HORSE:0.12);
+
+
+ TIME STAMP
+--- a/tests/check-qp-tn-nucl
++++ b/tests/check-qp-tn-nucl
+@@ -53,12 +53,12 @@ Y/R transition parameter (estimated from
+
+ Rate matrix R (parameters restricted to selected model):
+
+- A-C rate: 1.00000
+- A-G rate: 1.54307
+- A-T rate: 1.00000
+- C-G rate: 1.00000
+- C-T rate: 3.45671
+- G-T rate: 1.00000
++ A-C rate: 1.00
++ A-G rate: 1.54
++ A-T rate: 1.00
++ C-G rate: 1.00
++ C-T rate: 3.45
++ G-T rate: 1.00
+
+ Nucleotide frequencies (estimated from data set):
+
+@@ -127,26 +127,26 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 8
+-Thylacinus 0.00000 0.25985 0.22390 0.25044 0.26641 0.25322 0.22626
+- 0.24180
+-Sarcophilu 0.25985 0.00000 0.13242 0.27396 0.28989 0.33153 0.26303
+- 0.30195
+-Dasyurus 0.22390 0.13242 0.00000 0.20339 0.25292 0.25452 0.17982
+- 0.24252
+-Echymipera 0.25044 0.27396 0.20339 0.00000 0.30315 0.34463 0.23492
+- 0.27794
+-Trichosuru 0.26641 0.28989 0.25292 0.30315 0.00000 0.21427 0.29184
+- 0.27804
+-Phalanger 0.25322 0.33153 0.25452 0.34463 0.21427 0.00000 0.29454
+- 0.33617
+-Philander 0.22626 0.26303 0.17982 0.23492 0.29184 0.29454 0.00000
+- 0.22765
+-Bos 0.24180 0.30195 0.24252 0.27794 0.27804 0.33617 0.22765
+- 0.00000
+-
+-Average distance (over all possible pairs of sequences): 0.25896
+- minimum : 0.13242, maximum : 0.34463
+- variance : 0.00217, std.dev. : 0.04660
++Thylacinus 0.00 0.25 0.22 0.25 0.26 0.25 0.22
++ 0.24
++Sarcophilu 0.25 0.00 0.13 0.27 0.28 0.33 0.26
++ 0.30
++Dasyurus 0.22 0.13 0.00 0.20 0.25 0.25 0.17
++ 0.24
++Echymipera 0.25 0.27 0.20 0.00 0.30 0.34 0.23
++ 0.27
++Trichosuru 0.26 0.28 0.25 0.30 0.00 0.21 0.29
++ 0.27
++Phalanger 0.25 0.33 0.25 0.34 0.21 0.00 0.29
++ 0.33
++Philander 0.22 0.26 0.17 0.23 0.29 0.29 0.00
++ 0.22
++Bos 0.24 0.30 0.24 0.27 0.27 0.33 0.22
++ 0.00
++
++Average distance (over all possible pairs of sequences): 0.25
++ minimum : 0.13, maximum : 0.34
++ variance : 0.00, std.dev. : 0.04
+
+
+ RATE HETEROGENEITY
+@@ -240,11 +240,11 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****..** : 1000 (1.000)
+- *..***** : 1000 (1.000)
+- *...**.. : 704 (0.704)
+- ******.. : 692 (0.692)
+- *...**** : 528 (0.528)
++ ****..** : 1000 (1.00)
++ *..***** : 1000 (1.00)
++ *...**.. : 704 (0.70)
++ ******.. : 692 (0.69)
++ *...**** : 528 (0.52)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+@@ -255,26 +255,26 @@ the consensus tree:
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ***.**.. : 191 (0.191)
+- *...**.* : 183 (0.183)
+- *..***.. : 128 (0.128)
+- ****..*. : 81 (0.081)
+- *.....** : 79 (0.079)
+- ***.**.* : 76 (0.076)
+- *..*..** : 68 (0.068)
+- ****.... : 58 (0.058)
+- *..*.... : 41 (0.041)
+- *......* : 39 (0.039)
+- *..***.* : 37 (0.037)
+- *...***. : 17 (0.017)
+- *.....*. : 16 (0.016)
+- ***..... : 14 (0.014)
+- ***.***. : 12 (0.012)
+- ***...** : 11 (0.011)
+- *..*..*. : 9 (0.009)
+- *..****. : 7 (0.007)
+- ***...*. : 4 (0.004)
+- *..*...* : 3 (0.003)
++ ***.**.. : 191 (0.19)
++ *...**.* : 183 (0.18)
++ *..***.. : 128 (0.12)
++ ****..*. : 81 (0.08)
++ *.....** : 79 (0.07)
++ ***.**.* : 76 (0.07)
++ *..*..** : 68 (0.06)
++ ****.... : 58 (0.05)
++ *..*.... : 41 (0.04)
++ *......* : 39 (0.03)
++ *..***.* : 37 (0.03)
++ *...***. : 17 (0.01)
++ *.....*. : 16 (0.01)
++ ***..... : 14 (0.01)
++ ***.***. : 12 (0.01)
++ ***...** : 11 (0.01)
++ *..*..*. : 9 (0.00)
++ *..****. : 7 (0.00)
++ ***...*. : 4 (0.00)
++ *..*...* : 3 (0.00)
+
+ (2 other less frequent bipartitions not shown)
+
+@@ -303,22 +303,22 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-Thylacinus 1 0.11294 0.03951 9 0.06396 0.03574
+-Sarcophilu 2 0.12830 0.03720 10 0.03927 0.02464
+-Dasyurus 3 0.01046 0.01329 11 0.06846 0.03213
+-Echymipera 4 0.13275 0.04059 12 0.02637 0.02260
+-Trichosuru 5 0.10847 0.03861 13 0.04080 0.02830
+-Phalanger 6 0.12347 0.04146
+-Philander 7 0.08552 0.03431 8 iterations until convergence
+-Bos 8 0.13891 0.04250 log L: -599.59
++Thylacinus 1 0.11 0.03 9 0.06 0.03
++Sarcophilu 2 0.12 0.03 10 0.03 0.02
++Dasyurus 3 0.01 0.01 11 0.06 0.03
++Echymipera 4 0.13 0.04 12 0.02 0.02
++Trichosuru 5 0.10 0.03 13 0.04 0.02
++Phalanger 6 0.12 0.04
++Philander 7 0.08 0.03 8 iterations until convergence
++Bos 8 0.13 0.04 log L: -599.59
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(Thylacinus:0.11294,(Trichosuru:0.10847,Phalanger:0.12347)100:0.06396,
+-((Philander:0.08552,Bos:0.13891)69:0.03927,((Sarcophilu:0.12830,
+-Dasyurus:0.01046)100:0.06846,Echymipera:0.13275)53:0.02637)70:0.04080);
++(Thylacinus:0.11,(Trichosuru:0.10,Phalanger:0.12)100:0.06,
++((Philander:0.08,Bos:0.13)69:0.03,((Sarcophilu:0.12,
++Dasyurus:0.01)100:0.06,Echymipera:0.13)53:0.02)70:0.04);
+
+
+ TIME STAMP
+--- a/tests/check-qp-vt-prot
++++ b/tests/check-qp-vt-prot
+@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.16783 0.85204 0.87347 1.69056 1.50964 2.05575
+-HBB_HORSE 0.16783 0.00000 0.87363 0.87544 1.67978 1.52916 2.09374
+-HBA_HUMAN 0.85204 0.87363 0.00000 0.11958 1.58540 1.13053 2.11864
+-HBA_HORSE 0.87347 0.87544 0.11958 0.00000 1.64085 1.18694 2.01999
+-MYG_PHYCA 1.69056 1.67978 1.58540 1.64085 0.00000 1.63531 2.09093
+-GLB5_PETMA 1.50964 1.52916 1.13053 1.18694 1.63531 0.00000 1.84636
+-LGB2_LUPLU 2.05575 2.09374 2.11864 2.01999 2.09093 1.84636 0.00000
+-
+-Average distance (over all possible pairs of sequences): 1.40836
+- minimum : 0.11958, maximum : 2.11864
+- variance : 0.36159, std.dev. : 0.60133
++HBB_HUMAN 0.00 0.16 0.85 0.87 1.69 1.50 2.05
++HBB_HORSE 0.16 0.00 0.87 0.87 1.67 1.52 2.09
++HBA_HUMAN 0.85 0.87 0.00 0.11 1.58 1.13 2.11
++HBA_HORSE 0.87 0.87 0.11 0.00 1.64 1.18 2.01
++MYG_PHYCA 1.69 1.67 1.58 1.64 0.00 1.63 2.09
++GLB5_PETMA 1.50 1.52 1.13 1.18 1.63 0.00 1.84
++LGB2_LUPLU 2.05 2.09 2.11 2.01 2.09 1.84 0.00
++
++Average distance (over all possible pairs of sequences): 1.40
++ minimum : 0.11, maximum : 2.11
++ variance : 0.36, std.dev. : 0.60
+
+
+ RATE HETEROGENEITY
+@@ -229,21 +229,21 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- **..*** : 1000 (1.000)
+- ****... : 1000 (1.000)
+- **..... : 1000 (1.000)
++ **..*** : 1000 (1.00)
++ ****... : 1000 (1.00)
++ **..... : 1000 (1.00)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****.*. : 347 (0.347)
++ ****.*. : 347 (0.34)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *****.. : 341 (0.341)
+- ****..* : 312 (0.312)
++ *****.. : 341 (0.34)
++ ****..* : 312 (0.31)
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
+@@ -268,21 +268,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04599 0.03062 8 0.25241 0.08069
+-HBB_HORSE 2 0.12231 0.03740 9 0.42027 0.11482
+-HBA_HUMAN 3 0.03150 0.02213 10 0.54295 0.10035
+-HBA_HORSE 4 0.08803 0.03011
+-MYG_PHYCA 5 1.02820 0.16336
+-GLB5_PETMA 6 0.60660 0.11823 11 iterations until convergence
+-LGB2_LUPLU 7 1.38557 0.20879 log L: -1703.59
++HBB_HUMAN 1 0.04 0.03 8 0.25 0.08
++HBB_HORSE 2 0.12 0.03 9 0.42 0.11
++HBA_HUMAN 3 0.03 0.02 10 0.54 0.10
++HBA_HORSE 4 0.08 0.03
++MYG_PHYCA 5 1.02 0.16
++GLB5_PETMA 6 0.60 0.11 11 iterations until convergence
++LGB2_LUPLU 7 1.38 0.20 log L: -1703.59
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04599,((HBA_HUMAN:0.03150,HBA_HORSE:0.08803)100:0.25241,
+-(MYG_PHYCA:1.02820,GLB5_PETMA:0.60660,LGB2_LUPLU:1.38557)100:0.42027)
+-100:0.54295,HBB_HORSE:0.12231);
++(HBB_HUMAN:0.04,((HBA_HUMAN:0.03,HBA_HORSE:0.08)100:0.25,
++(MYG_PHYCA:1.02,GLB5_PETMA:0.60,LGB2_LUPLU:1.38)100:0.42)
++100:0.54,HBB_HORSE:0.12);
+
+
+ TIME STAMP
+--- a/tests/check-qp-wag-prot
++++ b/tests/check-qp-wag-prot
+@@ -128,17 +128,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.16900 0.89717 0.92939 1.84037 1.59398 2.23038
+-HBB_HORSE 0.16900 0.00000 0.92202 0.93317 1.80081 1.60452 2.27765
+-HBA_HUMAN 0.89717 0.92202 0.00000 0.12400 1.71106 1.17087 2.28564
+-HBA_HORSE 0.92939 0.93317 0.12400 0.00000 1.77692 1.23977 2.22372
+-MYG_PHYCA 1.84037 1.80081 1.71106 1.77692 0.00000 1.72932 2.25004
+-GLB5_PETMA 1.59398 1.60452 1.17087 1.23977 1.72932 0.00000 1.91159
+-LGB2_LUPLU 2.23038 2.27765 2.28564 2.22372 2.25004 1.91159 0.00000
+-
+-Average distance (over all possible pairs of sequences): 1.50578
+- minimum : 0.12400, maximum : 2.28564
+- variance : 0.42979, std.dev. : 0.65558
++HBB_HUMAN 0.00 0.16 0.89 0.92 1.84 1.59 2.23
++HBB_HORSE 0.16 0.00 0.92 0.93 1.80 1.60 2.27
++HBA_HUMAN 0.89 0.92 0.00 0.12 1.71 1.17 2.28
++HBA_HORSE 0.92 0.93 0.12 0.00 1.77 1.23 2.22
++MYG_PHYCA 1.84 1.80 1.71 1.77 0.00 1.72 2.25
++GLB5_PETMA 1.59 1.60 1.17 1.23 1.72 0.00 1.91
++LGB2_LUPLU 2.23 2.27 2.28 2.22 2.25 1.91 0.00
++
++Average distance (over all possible pairs of sequences): 1.50
++ minimum : 0.12, maximum : 2.28
++ variance : 0.42, std.dev. : 0.65
+
+
+ RATE HETEROGENEITY
+@@ -229,21 +229,21 @@ trees that have been generated in the 10
+ Bipartitions included in the quartet puzzling tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- **..*** : 1000 (1.000)
+- ****... : 1000 (1.000)
+- **..... : 1000 (1.000)
++ **..*** : 1000 (1.00)
++ ****... : 1000 (1.00)
++ **..... : 1000 (1.00)
+
+ Congruent bipartitions occurred in 50% or less, not included in
+ the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- ****.*. : 347 (0.347)
++ ****.*. : 347 (0.34)
+
+ Incongruent bipartitions not included in the consensus tree:
+ (bipartition with sequences in input order : number of times seen (and ratio))
+
+- *****.. : 341 (0.341)
+- ****..* : 312 (0.312)
++ *****.. : 341 (0.34)
++ ****..* : 312 (0.31)
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS ON CONSENSUS TREE (NO CLOCK)
+@@ -268,21 +268,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.05028 0.03102 8 0.25788 0.08204
+-HBB_HORSE 2 0.11946 0.03740 9 0.44299 0.11946
+-HBA_HUMAN 3 0.02934 0.02189 10 0.57110 0.10504
+-HBA_HORSE 4 0.09430 0.03146
+-MYG_PHYCA 5 1.11239 0.17630
+-GLB5_PETMA 6 0.59341 0.11994 11 iterations until convergence
+-LGB2_LUPLU 7 1.46501 0.22199 log L: -1699.78
++HBB_HUMAN 1 0.05 0.03 8 0.25 0.08
++HBB_HORSE 2 0.11 0.03 9 0.44 0.11
++HBA_HUMAN 3 0.02 0.02 10 0.57 0.10
++HBA_HORSE 4 0.09 0.03
++MYG_PHYCA 5 1.11 0.17
++GLB5_PETMA 6 0.59 0.11 11 iterations until convergence
++LGB2_LUPLU 7 1.46 0.22 log L: -1699.78
+
+
+ Consensus tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.05028,((HBA_HUMAN:0.02934,HBA_HORSE:0.09430)100:0.25788,
+-(MYG_PHYCA:1.11239,GLB5_PETMA:0.59341,LGB2_LUPLU:1.46501)100:0.44299)
+-100:0.57110,HBB_HORSE:0.11946);
++(HBB_HUMAN:0.05,((HBA_HUMAN:0.02,HBA_HORSE:0.09)100:0.25,
++(MYG_PHYCA:1.11,GLB5_PETMA:0.59,LGB2_LUPLU:1.46)100:0.44)
++100:0.57,HBB_HORSE:0.11);
+
+
+ TIME STAMP
+--- a/tests/check-ut-pure-prot
++++ b/tests/check-ut-pure-prot
+@@ -129,17 +129,17 @@ Maximum likelihood distances are compute
+ substitution and rate heterogeneity.
+
+ 7
+-HBB_HUMAN 0.00000 0.17425 0.96068 0.99267 2.12932 1.77231 2.78644
+-HBB_HORSE 0.17425 0.00000 1.01062 1.02118 2.09456 1.78465 2.86187
+-HBA_HUMAN 0.96068 1.01062 0.00000 0.12147 1.93540 1.30123 2.54730
+-HBA_HORSE 0.99267 1.02118 0.12147 0.00000 2.00515 1.39193 2.51172
+-MYG_PHYCA 2.12932 2.09456 1.93540 2.00515 0.00000 2.12347 2.79386
+-GLB5_PETMA 1.77231 1.78465 1.30123 1.39193 2.12347 0.00000 2.18272
+-LGB2_LUPLU 2.78644 2.86187 2.54730 2.51172 2.79386 2.18272 0.00000
+-
+-Average distance (over all possible pairs of sequences): 1.73823
+- minimum : 0.12147, maximum : 2.86187
+- variance : 0.65214, std.dev. : 0.80755
++HBB_HUMAN 0.00 0.17 0.96 0.99 2.12 1.77 2.78
++HBB_HORSE 0.17 0.00 1.01 1.02 2.09 1.78 2.86
++HBA_HUMAN 0.96 1.01 0.00 0.12 1.93 1.30 2.54
++HBA_HORSE 0.99 1.02 0.12 0.00 2.00 1.39 2.51
++MYG_PHYCA 2.12 2.09 1.93 2.00 0.00 2.12 2.79
++GLB5_PETMA 1.77 1.78 1.30 1.39 2.12 0.00 2.18
++LGB2_LUPLU 2.78 2.86 2.54 2.51 2.79 2.18 0.00
++
++Average distance (over all possible pairs of sequences): 1.73
++ minimum : 0.12, maximum : 2.86
++ variance : 0.65, std.dev. : 0.80
+
+
+ RATE HETEROGENEITY
+@@ -174,13 +174,13 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04834 0.03148 8 0.28039 0.08746
+-HBB_HORSE 2 0.12686 0.03876 9 0.00001 0.00100
+-HBA_HUMAN 3 0.02653 0.02208 10 0.40361 0.12824
+-HBA_HORSE 4 0.09440 0.03145 11 0.60481 0.11282
+-MYG_PHYCA 5 1.33106 0.21114
+-GLB5_PETMA 6 0.70107 0.14140 9 iterations until convergence
+-LGB2_LUPLU 7 1.76830 0.28198 log L: -1699.50
++HBB_HUMAN 1 0.04 0.03 8 0.28 0.08
++HBB_HORSE 2 0.12 0.03 9 0.00 0.00
++HBA_HUMAN 3 0.02 0.02 10 0.40 0.12
++HBA_HORSE 4 0.09 0.03 11 0.60 0.11
++MYG_PHYCA 5 1.33 0.21
++GLB5_PETMA 6 0.70 0.14 9 iterations until convergence
++LGB2_LUPLU 7 1.76 0.28 log L: -1699.50
+
+ WARNING --- at least one branch length is close to an internal boundary!
+
+@@ -188,9 +188,9 @@ WARNING --- at least one branch length i
+ Unrooted user defined tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04834,HBB_HORSE:0.12686,((HBA_HUMAN:0.02653,HBA_HORSE:0.09440)
+-:0.28039,((MYG_PHYCA:1.33106,GLB5_PETMA:0.70107):0.00001,LGB2_LUPLU:1.76830)
+-:0.40361):0.60481);
++(HBB_HUMAN:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09)
++:0.28,((MYG_PHYCA:1.33,GLB5_PETMA:0.70):0.00,LGB2_LUPLU:1.76)
++:0.40):0.60);
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 2 (NO CLOCK)
+@@ -215,21 +215,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04915 0.03158 8 0.28347 0.08778
+-HBB_HORSE 2 0.12604 0.03871 9 0.18149 0.13086
+-HBA_HUMAN 3 0.02555 0.02185 10 0.34695 0.12552
+-HBA_HORSE 4 0.09541 0.03153 11 0.60238 0.11261
+-MYG_PHYCA 5 1.33157 0.21115
+-GLB5_PETMA 6 0.57473 0.13844 9 iterations until convergence
+-LGB2_LUPLU 7 1.71340 0.27647 log L: -1699.00
++HBB_HUMAN 1 0.04 0.03 8 0.28 0.08
++HBB_HORSE 2 0.12 0.03 9 0.18 0.13
++HBA_HUMAN 3 0.02 0.02 10 0.34 0.12
++HBA_HORSE 4 0.09 0.03 11 0.60 0.11
++MYG_PHYCA 5 1.33 0.21
++GLB5_PETMA 6 0.57 0.13 9 iterations until convergence
++LGB2_LUPLU 7 1.71 0.27 log L: -1699.00
+
+
+ Unrooted user defined tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04915,HBB_HORSE:0.12604,((HBA_HUMAN:0.02555,HBA_HORSE:0.09541)
+-:0.28347,(MYG_PHYCA:1.33157,(GLB5_PETMA:0.57473,LGB2_LUPLU:1.71340)
+-:0.18149):0.34695):0.60238);
++(HBB_HUMAN:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09)
++:0.28,(MYG_PHYCA:1.33,(GLB5_PETMA:0.57,LGB2_LUPLU:1.71)
++:0.18):0.34):0.60);
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 3 (NO CLOCK)
+@@ -254,21 +254,21 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04869 0.03153 8 0.27871 0.08717
+-HBB_HORSE 2 0.12653 0.03874 9 0.12334 0.15661
+-HBA_HUMAN 3 0.02634 0.02204 10 0.39110 0.12780
+-HBA_HORSE 4 0.09459 0.03147 11 0.60627 0.11286
+-MYG_PHYCA 5 1.22880 0.20960
+-GLB5_PETMA 6 0.69972 0.14141 11 iterations until convergence
+-LGB2_LUPLU 7 1.68480 0.28106 log L: -1699.32
++HBB_HUMAN 1 0.04 0.03 8 0.27 0.08
++HBB_HORSE 2 0.12 0.03 9 0.12 0.15
++HBA_HUMAN 3 0.02 0.02 10 0.39 0.12
++HBA_HORSE 4 0.09 0.03 11 0.60 0.11
++MYG_PHYCA 5 1.22 0.20
++GLB5_PETMA 6 0.69 0.14 11 iterations until convergence
++LGB2_LUPLU 7 1.68 0.28 log L: -1699.32
+
+
+ Unrooted user defined tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04869,HBB_HORSE:0.12653,((HBA_HUMAN:0.02634,HBA_HORSE:0.09459)
+-:0.27871,((MYG_PHYCA:1.22880,LGB2_LUPLU:1.68480):0.12334,GLB5_PETMA:0.69972)
+-:0.39110):0.60627);
++(HBB_HUMAN:0.04,HBB_HORSE:0.12,((HBA_HUMAN:0.02,HBA_HORSE:0.09)
++:0.27,((MYG_PHYCA:1.22,LGB2_LUPLU:1.68):0.12,GLB5_PETMA:0.69)
++:0.39):0.60);
+
+
+ MAXIMUM LIKELIHOOD BRANCH LENGTHS OF USER DEFINED TREE # 4 (NO CLOCK)
+@@ -293,30 +293,30 @@ substitution and rate heterogeneity.
+
+
+ branch length S.E. branch length S.E.
+-HBB_HUMAN 1 0.04834 0.03148 8 0.40364 0.12824
+-HBB_HORSE 2 0.12685 0.03876 9 0.28040 0.08746
+-HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281
+-HBA_HORSE 4 0.09440 0.03145
+-MYG_PHYCA 5 1.33095 0.21112
+-GLB5_PETMA 6 0.70107 0.14140 10 iterations until convergence
+-LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50
++HBB_HUMAN 1 0.04 0.03 8 0.40 0.12
++HBB_HORSE 2 0.12 0.03 9 0.28 0.08
++HBA_HUMAN 3 0.02 0.02 10 0.60 0.11
++HBA_HORSE 4 0.09 0.03
++MYG_PHYCA 5 1.33 0.21
++GLB5_PETMA 6 0.70 0.14 10 iterations until convergence
++LGB2_LUPLU 7 1.76 0.28 log L: -1699.50
+
+
+ Unrooted user defined tree with maximum likelihood branch lengths
+ (in CLUSTAL W notation):
+
+-(HBB_HUMAN:0.04834,((MYG_PHYCA:1.33095,GLB5_PETMA:0.70107,LGB2_LUPLU:1.76831)
+-:0.40364,(HBA_HUMAN:0.02653,HBA_HORSE:0.09440):0.28040):0.60481,HBB_HORSE:0.12685);
++(HBB_HUMAN:0.04,((MYG_PHYCA:1.33,GLB5_PETMA:0.70,LGB2_LUPLU:1.76)
++:0.40,(HBA_HUMAN:0.02,HBA_HORSE:0.09):0.28):0.60,HBB_HORSE:0.12);
+
+
+ COMPARISON OF USER TREES (NO CLOCK)
+
+ Tree log L difference S.E. p-1sKH p-SH c-ELW 2sKH
+ -------------------------------------------------------------------------------
+- 1 -1699.50 0.49 1.0266 0.3150 + 0.4600 + 0.1871 + +
+- 2 -1699.00 0.00 <---- best 1.0000 + 1.0000 + 0.3643 + best
+- 3 -1699.32 0.32 1.3440 0.3950 + 0.4830 + 0.2614 + +
+- 4 -1699.50 0.49 1.0267 0.3350 + 0.4600 + 0.1871 + +
++ 1 -1699.50 0.49 1.02 0.31 + 0.46 + 0.18 + +
++ 2 -1699.00 0.00 <---- best 1.00 + 1.00 + 0.36 + best
++ 3 -1699.32 0.32 1.34 0.39 + 0.48 + 0.26 + +
++ 4 -1699.50 0.49 1.02 0.33 + 0.46 + 0.18 + +
+
+ The columns show the results and p-values of the following tests:
+ 1sKH - one sided KH test based on pairwise SH tests (Shimodaira-Hasegawa
+--- a/tests/cons-pure-prot.test
++++ b/tests/cons-pure-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/lm-pure-prot.test
++++ b/tests/lm-pure-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-clock.test
++++ b/tests/qp-clock.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-hky-clock-nucl.test
++++ b/tests/qp-hky-clock-nucl.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-hky-rhet-clock-nucl.test
++++ b/tests/qp-hky-rhet-clock-nucl.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-hky-rhet-nucl.test
++++ b/tests/qp-hky-rhet-nucl.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-jtt-prot.test
++++ b/tests/qp-jtt-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-jtt-rhet-clock-prot.test
++++ b/tests/qp-jtt-rhet-clock-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-jtt-rhet-prot.test
++++ b/tests/qp-jtt-rhet-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-mtrev-prot.test
++++ b/tests/qp-mtrev-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-pure-bin.test
++++ b/tests/qp-pure-bin.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-pure-nucl.test
++++ b/tests/qp-pure-nucl.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-pure-prot.test
++++ b/tests/qp-pure-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-tn-nucl.test
++++ b/tests/qp-tn-nucl.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-vt-prot.test
++++ b/tests/qp-vt-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/qp-wag-prot.test
++++ b/tests/qp-wag-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/template-test
++++ b/tests/template-test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
+--- a/tests/ut-pure-prot.test
++++ b/tests/ut-pure-prot.test
+@@ -229,6 +229,7 @@ if test $GENERATE -eq 1; then
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > check-${TEST_PREF}
+ exit 0
+ else
+@@ -238,6 +239,7 @@ else
+ | grep -v "^Date and time" \
+ | grep -v "^Runtime (" \
+ | sed -e "s/$VVV//g" \
++ | sed -e "s/\([0-9]\.[0-9][0-9]\)[0-9]\+/\1/g" \
+ > ${RESULT_PREF}.clean
+ diff ${RESULT_PREF}.clean check-${TEST_PREF}
+ result=$?
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ spelling.patch
fix-mpi3-build.patch
update_test_results.patch
reproducible-build.patch
+reduce_decimals_for_testing.patch
View it on GitLab: https://salsa.debian.org/med-team/tree-puzzle/-/commit/0e46614b97522bffaf734ca9e8bb78d211712f95
--
View it on GitLab: https://salsa.debian.org/med-team/tree-puzzle/-/commit/0e46614b97522bffaf734ca9e8bb78d211712f95
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