diff --git a/test/paml/unrooted_absent/association/1_trio_ML.asso b/test/paml/unrooted_absent/association/1_trio_ML.asso
index f67c13d4a80f650e7aeb8f1de51553d797c915fe..077f5d6e37d7a458fbafe8a9a7c9b06b48dfadbd 100644
--- a/test/paml/unrooted_absent/association/1_trio_ML.asso
+++ b/test/paml/unrooted_absent/association/1_trio_ML.asso
@@ -24,14 +24,14 @@
-----* 60+(61)+(42) case/control:200/200
|
| [0] ddl=3 chi2=6.69 p_value_chi2=0.0824
- | [1] ddl=6 chi2=10.87 p_value_chi2=0.07
- | [2] ddl=6 chi2=20.30 p_value_chi2=0.002
- | [3] ddl=11 chi2=21.62 p_value_chi2=0.013
- | [4] ddl=6 chi2=23.18 p_value_chi2=0
- | [5] ddl=5 chi2=23.07 p_value_chi2=0
- | [6] ddl=6 chi2=20.13 p_value_chi2=0
- | [7] ddl=1 chi2=1.66 p_value_chi2=0.392
- | [8] ddl=1 chi2=1.35 p_value_chi2=0.33
+ | [1] ddl=7 chi2=11.30 p_value_chi2=0.102
+ | [2] ddl=11 chi2=24.02 p_value_chi2=0.007
+ | [3] ddl=20 chi2=39.11 p_value_chi2=0.001
+ | [4] ddl=24 chi2=54.71 p_value_chi2=0.001
+ | [5] ddl=28 chi2=63.21 p_value_chi2=0
+ | [6] ddl=32 chi2=65.94 p_value_chi2=0
+ | [7] ddl=33 chi2=67.18 p_value_chi2=0
+ | [8] ddl=34 chi2=68.34 p_value_chi2=0
| /----* H010 case/control:1/3
| /----* 53 case/control:1/4
| | | Site: 10 Sens: C-->G
diff --git a/test/paml/unrooted_absent/association/2base.t b/test/paml/unrooted_absent/association/2base.t
index 440309570493f495d98b528146668ffaef391eb0..3c69e532ef866ce4c66f2a5be8a28ec7de0e004c 100644
--- a/test/paml/unrooted_absent/association/2base.t
+++ b/test/paml/unrooted_absent/association/2base.t
@@ -2,36 +2,36 @@
H019
H026 9.0000
H004 nan nan
-H020 nan 9.0000 9.0000
-H034 nan 9.0000 nan nan
-H027 nan 9.0000 9.0000 nan nan
-H023 9.0000 nan nan 9.0000 9.0000 nan
+H020 9.0000 9.0000 9.0000
+H034 nan 9.0000 9.0000 nan
+H027 9.0000 9.0000 9.0000 nan nan
+H023 9.0000 nan nan 9.0000 9.0000 9.0000
H016 nan nan nan 9.0000 9.0000 9.0000 nan
-H002 9.0000 nan nan 9.0000 9.0000 nan nan nan
-H015 nan 9.0000 nan nan nan 9.0000 nan 9.0000 9.0000
-H006 9.0000 nan nan nan 9.0000 9.0000 nan 9.0000 nan nan
-H001 nan 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 nan nan
-H010 nan 9.0000 9.0000 nan nan nan nan 9.0000 9.0000 nan 9.0000 nan
-H028 nan 9.0000 nan nan nan 9.0000 nan 9.0000 9.0000 nan nan nan nan
-H024 nan nan nan 9.0000 nan 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000 nan
+H002 9.0000 nan nan 9.0000 9.0000 9.0000 nan nan
+H015 9.0000 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000
+H006 9.0000 nan nan nan 9.0000 9.0000 nan 9.0000 9.0000 nan
+H001 nan 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000 nan nan
+H010 9.0000 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 nan 9.0000 nan
+H028 9.0000 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000 nan nan nan nan
+H024 nan 9.0000 nan 9.0000 9.0000 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000 9.0000
H017 9.0000 nan 9.0000 nan nan nan nan 9.0000 9.0000 nan 9.0000 nan nan nan 9.0000
-H009 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan nan nan nan 9.0000 nan 9.0000 9.0000 nan
-H007 9.0000 nan nan 9.0000 9.0000 9.0000 nan nan nan nan nan nan nan nan nan nan nan
-H033 nan nan 9.0000 nan nan nan 9.0000 9.0000 9.0000 nan 9.0000 nan nan nan 9.0000 nan 9.0000 nan
-H008 nan nan nan 9.0000 9.0000 9.0000 nan nan nan 9.0000 nan 9.0000 9.0000 9.0000 nan 9.0000 nan nan 9.0000
-H029 nan nan nan nan nan nan 9.0000 9.0000 9.0000 nan nan nan nan nan nan nan 9.0000 nan nan nan
-H003 nan 9.0000 nan nan nan nan 9.0000 nan 9.0000 nan 9.0000 nan nan nan nan nan 9.0000 nan nan 9.0000 nan
-H035 9.0000 nan nan nan nan nan nan nan nan nan nan 9.0000 nan nan 9.0000 nan nan nan nan 9.0000 9.0000 nan
-H013 nan 9.0000 nan nan nan nan 9.0000 nan 9.0000 9.0000 9.0000 nan nan 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan nan 9.0000
-H032 nan nan nan 9.0000 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan nan nan nan nan nan nan nan
-H025 nan nan nan 9.0000 nan 9.0000 nan nan nan nan nan nan 9.0000 nan nan 9.0000 nan nan nan nan nan 9.0000 nan 9.0000 nan
-H021 nan nan nan 9.0000 9.0000 nan nan nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan nan 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan
-H030 nan nan nan nan nan 9.0000 nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan nan 9.0000 9.0000 nan 9.0000
-H031 nan nan nan 9.0000 nan 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan nan 9.0000 nan nan nan 9.0000 nan nan nan nan nan
-H012 9.0000 nan nan 9.0000 9.0000 nan nan nan nan 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan nan 9.0000 nan 9.0000 9.0000 nan 9.0000 nan nan nan nan nan
+H009 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 9.0000 nan
+H007 9.0000 nan nan 9.0000 9.0000 9.0000 nan nan nan nan nan 9.0000 nan nan 9.0000 nan nan
+H033 nan 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 nan nan 9.0000 9.0000 nan 9.0000 9.0000
+H008 nan nan nan 9.0000 9.0000 9.0000 9.0000 nan nan 9.0000 nan 9.0000 9.0000 9.0000 nan 9.0000 9.0000 nan 9.0000
+H029 nan 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan nan nan nan nan 9.0000 9.0000 nan 9.0000
+H003 nan 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan nan nan 9.0000 9.0000 9.0000 nan nan 9.0000 nan
+H035 9.0000 nan nan 9.0000 9.0000 9.0000 nan nan nan 9.0000 nan 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000
+H013 nan 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan nan 9.0000
+H032 nan nan nan 9.0000 9.0000 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 nan 9.0000 9.0000 nan 9.0000 nan 9.0000 nan 9.0000 nan
+H025 9.0000 nan nan 9.0000 nan 9.0000 nan nan 9.0000 nan nan 9.0000 9.0000 nan nan 9.0000 9.0000 nan 9.0000 nan nan 9.0000 nan 9.0000 nan
+H021 nan nan nan 9.0000 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan 9.0000 9.0000 nan 9.0000 9.0000 9.0000 9.0000 nan 9.0000
+H030 9.0000 nan nan nan nan 9.0000 nan 9.0000 9.0000 nan nan nan nan nan nan nan 9.0000 nan 9.0000 nan nan nan nan 9.0000 9.0000 nan 9.0000
+H031 nan 9.0000 nan 9.0000 9.0000 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan 9.0000 9.0000 nan nan 9.0000 9.0000 nan nan nan nan 9.0000
+H012 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan nan 9.0000 nan 9.0000 9.0000 9.0000 9.0000 nan nan nan 9.0000 nan 9.0000 9.0000 nan 9.0000 nan nan nan nan 9.0000
H005 nan 9.0000 nan 9.0000 9.0000 9.0000 9.0000 nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 nan 9.0000 9.0000 9.0000 9.0000 nan 9.0000 9.0000 nan nan nan nan nan 9.0000 nan 9.0000
-H011 nan nan 9.0000 nan nan nan nan 9.0000 9.0000 nan nan nan nan nan 9.0000 nan nan nan nan 9.0000 nan nan nan nan nan nan 9.0000 nan 9.0000 nan 9.0000
-H022 nan 9.0000 nan nan nan nan 9.0000 9.0000 9.0000 nan 9.0000 nan nan nan nan 9.0000 9.0000 9.0000 nan nan nan nan 9.0000 nan nan nan 9.0000 nan nan 9.0000 nan nan
-H014 nan nan 9.0000 nan nan nan nan 9.0000 9.0000 nan 9.0000 nan nan nan 9.0000 nan nan nan nan 9.0000 nan nan 9.0000 nan nan nan nan nan 9.0000 nan 9.0000 nan nan
-H018 nan 9.0000 nan nan nan nan nan 9.0000 9.0000 nan nan nan nan nan nan nan nan nan nan 9.0000 nan nan nan nan 9.0000 nan 9.0000 nan nan 9.0000 9.0000 nan nan nan
-OUTG 9.0000 nan nan 9.0000 9.0000 9.0000 nan nan nan nan nan nan 9.0000 nan nan 9.0000 nan nan 9.0000 nan nan 9.0000 nan 9.0000 9.0000 nan 9.0000 nan nan nan 9.0000 nan 9.0000 9.0000 nan
+H011 nan 9.0000 9.0000 nan nan nan nan 9.0000 9.0000 nan 9.0000 nan nan nan 9.0000 nan nan nan nan 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 nan 9.0000 9.0000 9.0000
+H022 nan 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 9.0000 9.0000 nan nan 9.0000 nan 9.0000 9.0000 9.0000 nan 9.0000 nan nan 9.0000 nan 9.0000 9.0000 9.0000 9.0000 nan 9.0000 nan nan
+H014 nan nan 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 9.0000 nan nan 9.0000 9.0000 nan nan 9.0000 nan 9.0000 nan 9.0000 9.0000 9.0000 9.0000 9.0000 nan 9.0000 9.0000 9.0000 9.0000 nan nan
+H018 nan 9.0000 9.0000 nan nan nan 9.0000 9.0000 9.0000 nan nan nan nan nan 9.0000 nan 9.0000 nan nan 9.0000 nan nan 9.0000 nan 9.0000 nan 9.0000 nan 9.0000 9.0000 9.0000 nan nan nan
+OUTG 9.0000 nan nan 9.0000 9.0000 9.0000 nan nan nan nan nan nan 9.0000 nan nan 9.0000 nan nan 9.0000 nan nan 9.0000 nan 9.0000 9.0000 nan 9.0000 nan nan nan nan nan 9.0000 9.0000 nan
diff --git a/test/paml/unrooted_absent/association/lnf b/test/paml/unrooted_absent/association/lnf
index 1677a53d22d2f74a066f020299de375c105fa2b1..85a4532d42e3b7aa9a1d6dd89d6564cb0536ebd7 100644
--- a/test/paml/unrooted_absent/association/lnf
+++ b/test/paml/unrooted_absent/association/lnf
@@ -1,16 +1,15 @@
- -1 11 11
+ -1 10 10
1
- 1 1 -21.8448847646 0.0000 GGGCGCCGCCCCCCGCCCGGGCCGGGGCGCGCGGCC
- 2 1 -13.6418393080 0.0000 CCCGCCCCCGGGCGCCCCCCCCCCCCCCCCCCCCCC
- 3 1 -11.6756376430 0.0001 GCGGGCCGCGGGGGGCCGGGGGGGGGCGGCGGGCGG
- 4 1 -15.6068374149 0.0000 GCGGGCCCCGGGCGGCCCCGGCCGCGCGGCGCGCGG
- 5 1 -15.9985356580 0.0000 CGCGGGGCCGGGGGCGGGGCGCGCCGCGCGCGCGGG
- 6 1 -18.0565869859 0.0000 GCCCCGCGGCCCCCGCGCCGCCCGGCGCGGGCCCCC
- 7 1 -11.4529895174 0.0001 CGGCCCGGGCGCCCGCGGCGCCGCCGGGGGGCCCCG
- 8 1 -14.7076669554 0.0000 CGGCCCGGGCGCCGGCCGCGCCGCGGCGCGGCCCCG
- 9 1 -13.3076620282 0.0000 CGGCCCGGGGGCCCCCGGCGCCGCGGGCGGGCCCCG
- 10 1 -25.2617214477 0.0000 CCCGGGCCCCCCGCCCCCGCCCGGCCCCCCGCGCCC
- 11 1 -6.4871501505 0.0168 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC
\ No newline at end of file
+ 1 1 -21.7701316508 0.0000 GGGCGCCGCCCCCCGCCCGGGCCGGGGCGCGCGGCC
+ 2 1 -13.4855220119 0.0000 CCCGCCCCCGGGCGCCCCCCCCCCCCCCCCCCCCCC
+ 3 1 -11.8101938263 0.0001 GCGGGCCGCGGGGGGCCGGGGGGGGGCGGCGGGCGG
+ 4 1 -15.5093284894 0.0000 GCGGGCCCCGGGCGGCCCCGGCCGCGCGGCGCGCGG
+ 5 1 -15.9586997510 0.0000 CGCGGGGCCGGGGGCGGGGCGCGCCGCGCGCGCGGG
+ 6 1 -18.0353689751 0.0000 GCCCCGCGGCCCCCGCGCCGCCCGGCGCGGGCCCCC
+ 7 1 -11.7888575463 0.0001 CGGCCCGGGCGCCCGCGGCGCCGCCGGGGGGCCCCG
+ 8 1 -14.6248990790 0.0000 CGGCCCGGGCGCCGGCCGCGCCGCGGCGCGGCCCCG
+ 9 1 -13.6573284377 0.0000 CGGCCCGGGGGCCCCCGGCGCCGCGGGCGGGCCCCG
+ 10 1 -24.9555331769 0.0000 CCCGGGCCCCCCGCCCCCGCCCGGCCCCCCGCGCCC
\ No newline at end of file
diff --git a/test/paml/unrooted_absent/association/mlb b/test/paml/unrooted_absent/association/mlb
index bf607ff79ab204450702ae146b7980a68e17c15a..0dbb9e13324bf978cbbf65607724599ed79da940 100644
--- a/test/paml/unrooted_absent/association/mlb
+++ b/test/paml/unrooted_absent/association/mlb
@@ -1,132 +1,132 @@
seed used = 30455833
-H019 GCGGCGCCCC G
-H026 GCCCGCGGGC G
-H004 GCGGCCGGGC G
-H020 CGGGGCCCCG G
-H034 GCGGGCCCCG G
-H027 CCCCGGCCCG G
-H023 CCCCGCGGGC G
-H016 GCGCCGGGGC G
-H002 CCCCCGGGGC G
-H015 CGGGGCCCGC G
-H006 CGGGGCGGGC G
-H001 CGGGGCCCCC G
-H010 CCGCGCCCCG G
-H028 CGGGGCCGCC G
-H024 GCGGCGGGCC G
-H017 CCCCGCCCCC G
-H009 CCCCGGGCGC G
-H007 CCGCGCGGGC G
-H033 GCGCGCCCCG G
-H008 GCGGCGGGGC G
-H029 GCGGGCCCCC G
-H003 CCGCCCCCCC G
-H035 CCGCGCGGGG G
-H013 GCGGCGCCCG G
-H032 GCGCCGCGGC G
-H025 GCGGGCGGGC G
-H021 GCCCCGGCGC G
-H030 CCGGGCGGCC G
-H031 GCGGCGGCGC G
-H012 CCCCGGGGGC G
-H005 GCGGCGGGGG G
-H011 CCGCGCCCCC G
-H022 GCGGCCCCCG G
-H014 GCCCGCCCCC G
-H018 CCGGGCCCCC G
-OUTG CCGGGCGGGC C
+H019 GCGGCGCCCC
+H026 GCCCGCGGGC
+H004 GCGGCCGGGC
+H020 CGGGGCCCCG
+H034 GCGGGCCCCG
+H027 CCCCGGCCCG
+H023 CCCCGCGGGC
+H016 GCGCCGGGGC
+H002 CCCCCGGGGC
+H015 CGGGGCCCGC
+H006 CGGGGCGGGC
+H001 CGGGGCCCCC
+H010 CCGCGCCCCG
+H028 CGGGGCCGCC
+H024 GCGGCGGGCC
+H017 CCCCGCCCCC
+H009 CCCCGGGCGC
+H007 CCGCGCGGGC
+H033 GCGCGCCCCG
+H008 GCGGCGGGGC
+H029 GCGGGCCCCC
+H003 CCGCCCCCCC
+H035 CCGCGCGGGG
+H013 GCGGCGCCCG
+H032 GCGCCGCGGC
+H025 GCGGGCGGGC
+H021 GCCCCGGCGC
+H030 CCGGGCGGCC
+H031 GCGGCGGCGC
+H012 CCCCGGGGGC
+H005 GCGGCGGGGG
+H011 CCGCGCCCCC
+H022 GCGGCCCCCG
+H014 GCCCGCCCCC
+H018 CCGGGCCCCC
+OUTG CCGGGCGGGC
BASEML (in paml 3.14, January 2004) trio2.phy REV Global clock
-ns = 36 ls = 11
-# site patterns = 11
- 1 1 1 1 1 1 1 1 1 1 1
-
-H019 GCGGCGCCCC G
-H026 ..CCGCGGG. .
-H004 .....CGGG. .
-H020 CG..GC...G .
-H034 ....GC...G .
-H027 C.CCG....G .
-H023 C.CCGCGGG. .
-H016 ...C..GGG. .
-H002 C.CC..GGG. .
-H015 CG..GC..G. .
-H006 CG..GCGGG. .
-H001 CG..GC.... .
-H010 C..CGC...G .
-H028 CG..GC.G.. .
-H024 ......GG.. .
-H017 C.CCGC.... .
-H009 C.CCG.G.G. .
-H007 C..CGCGGG. .
-H033 ...CGC...G .
-H008 ......GGG. .
-H029 ....GC.... .
-H003 C..C.C.... .
-H035 C..CGCGGGG .
-H013 .........G .
-H032 ...C...GG. .
-H025 ....GCGGG. .
-H021 ..CC..G.G. .
-H030 C...GCGG.. .
-H031 ......G.G. .
-H012 C.CCG.GGG. .
-H005 ......GGGG .
-H011 C..CGC.... .
-H022 .....C...G .
-H014 ..CCGC.... .
-H018 C...GC.... .
-OUTG C...GCGGG. C
+ns = 36 ls = 10
+# site patterns = 10
+ 1 1 1 1 1 1 1 1 1 1
+
+H019 GCGGCGCCCC
+H026 ..CCGCGGG.
+H004 .....CGGG.
+H020 CG..GC...G
+H034 ....GC...G
+H027 C.CCG....G
+H023 C.CCGCGGG.
+H016 ...C..GGG.
+H002 C.CC..GGG.
+H015 CG..GC..G.
+H006 CG..GCGGG.
+H001 CG..GC....
+H010 C..CGC...G
+H028 CG..GC.G..
+H024 ......GG..
+H017 C.CCGC....
+H009 C.CCG.G.G.
+H007 C..CGCGGG.
+H033 ...CGC...G
+H008 ......GGG.
+H029 ....GC....
+H003 C..C.C....
+H035 C..CGCGGGG
+H013 .........G
+H032 ...C...GG.
+H025 ....GCGGG.
+H021 ..CC..G.G.
+H030 C...GCGG..
+H031 ......G.G.
+H012 C.CCG.GGG.
+H005 ......GGGG
+H011 C..CGC....
+H022 .....C...G
+H014 ..CCGC....
+H018 C...GC....
+OUTG C...GCGGG.
Frequencies..
T C A G
-H019 0.0000 0.5455 0.0000 0.4545
-H026 0.0000 0.4545 0.0000 0.5455
-H004 0.0000 0.3636 0.0000 0.6364
-H020 0.0000 0.4545 0.0000 0.5455
-H034 0.0000 0.4545 0.0000 0.5455
-H027 0.0000 0.6364 0.0000 0.3636
-H023 0.0000 0.5455 0.0000 0.4545
-H016 0.0000 0.3636 0.0000 0.6364
-H002 0.0000 0.5455 0.0000 0.4545
-H015 0.0000 0.4545 0.0000 0.5455
-H006 0.0000 0.2727 0.0000 0.7273
-H001 0.0000 0.5455 0.0000 0.4545
-H010 0.0000 0.6364 0.0000 0.3636
-H028 0.0000 0.4545 0.0000 0.5455
-H024 0.0000 0.3636 0.0000 0.6364
-H017 0.0000 0.8182 0.0000 0.1818
-H009 0.0000 0.5455 0.0000 0.4545
-H007 0.0000 0.4545 0.0000 0.5455
-H033 0.0000 0.5455 0.0000 0.4545
-H008 0.0000 0.2727 0.0000 0.7273
-H029 0.0000 0.5455 0.0000 0.4545
-H003 0.0000 0.8182 0.0000 0.1818
-H035 0.0000 0.3636 0.0000 0.6364
-H013 0.0000 0.4545 0.0000 0.5455
-H032 0.0000 0.4545 0.0000 0.5455
-H025 0.0000 0.2727 0.0000 0.7273
-H021 0.0000 0.5455 0.0000 0.4545
-H030 0.0000 0.4545 0.0000 0.5455
-H031 0.0000 0.3636 0.0000 0.6364
-H012 0.0000 0.4545 0.0000 0.5455
-H005 0.0000 0.1818 0.0000 0.8182
-H011 0.0000 0.7273 0.0000 0.2727
-H022 0.0000 0.5455 0.0000 0.4545
-H014 0.0000 0.7273 0.0000 0.2727
-H018 0.0000 0.6364 0.0000 0.3636
-OUTG 0.0000 0.4545 0.0000 0.5455
-
-Average 0.0000 0.4924 0.0000 0.5076
+H019 0.0000 0.6000 0.0000 0.4000
+H026 0.0000 0.5000 0.0000 0.5000
+H004 0.0000 0.4000 0.0000 0.6000
+H020 0.0000 0.5000 0.0000 0.5000
+H034 0.0000 0.5000 0.0000 0.5000
+H027 0.0000 0.7000 0.0000 0.3000
+H023 0.0000 0.6000 0.0000 0.4000
+H016 0.0000 0.4000 0.0000 0.6000
+H002 0.0000 0.6000 0.0000 0.4000
+H015 0.0000 0.5000 0.0000 0.5000
+H006 0.0000 0.3000 0.0000 0.7000
+H001 0.0000 0.6000 0.0000 0.4000
+H010 0.0000 0.7000 0.0000 0.3000
+H028 0.0000 0.5000 0.0000 0.5000
+H024 0.0000 0.4000 0.0000 0.6000
+H017 0.0000 0.9000 0.0000 0.1000
+H009 0.0000 0.6000 0.0000 0.4000
+H007 0.0000 0.5000 0.0000 0.5000
+H033 0.0000 0.6000 0.0000 0.4000
+H008 0.0000 0.3000 0.0000 0.7000
+H029 0.0000 0.6000 0.0000 0.4000
+H003 0.0000 0.9000 0.0000 0.1000
+H035 0.0000 0.4000 0.0000 0.6000
+H013 0.0000 0.5000 0.0000 0.5000
+H032 0.0000 0.5000 0.0000 0.5000
+H025 0.0000 0.3000 0.0000 0.7000
+H021 0.0000 0.6000 0.0000 0.4000
+H030 0.0000 0.5000 0.0000 0.5000
+H031 0.0000 0.4000 0.0000 0.6000
+H012 0.0000 0.5000 0.0000 0.5000
+H005 0.0000 0.2000 0.0000 0.8000
+H011 0.0000 0.8000 0.0000 0.2000
+H022 0.0000 0.6000 0.0000 0.4000
+H014 0.0000 0.8000 0.0000 0.2000
+H018 0.0000 0.7000 0.0000 0.3000
+OUTG 0.0000 0.4000 0.0000 0.6000
+
+Average 0.0000 0.5389 0.0000 0.4611
# constant sites: 0 (0.00%)
-ln Lmax (unconstrained) = -26.376848
+ln Lmax (unconstrained) = -23.025851
Distances: TN93 (kappa) (alpha set at 0.00)
This matrix is not used in later m.l. analysis.
@@ -134,60 +134,61 @@ This matrix is not used in later m.l. analysis.
H019
H026 9.0000( 0.0000)
H004 nan(999.0000) nan(999.0000)
-H020 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000)
-H034 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
-H027 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
-H023 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
+H020 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000)
+H034 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
+H027 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
+H023 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000)
H016 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
-H002 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
-H015 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000)
-H006 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
-H001 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
-H010 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000)
-H028 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
-H024 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
+H002 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
+H015 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000)
+H006 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
+H001 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
+H010 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000)
+H028 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
+H024 nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000)
H017 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000)
-H009 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
-H007 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
-H033 nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000)
-H008 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000)
-H029 nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
-H003 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000)
-H035 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
-H013 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000)
-H032 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
-H025 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000)
-H021 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
-H030 nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000)
-H031 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
-H012 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
+H009 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
+H007 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
+H033 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000)
+H008 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000)
+H029 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000)
+H003 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000)
+H035 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000)
+H013 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000)
+H032 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000)
+H025 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000)
+H021 nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000)
+H030 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000)
+H031 nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000)
+H012 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000)
H005 nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000)
-H011 nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000)
-H022 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
-H014 nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
-H018 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
-OUTG 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
-
-TREE # 1: (((((((((((((((((13, 19), (6, (16, 34))), 32), 22), 35), (((33, (24, 1)), 5), 21)), 4), 12), 10), 14), 28), ((11, ((((((29, 31), (25, 8)), 20), 15), 3), 26)), 36)), 23), 18), (2, 7)), 30), (27, 9), 17); MP score: 39.00
-lnL(ntime: 34 np: 39): -168.041512 +0.000000
+H011 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000)
+H022 nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
+H014 nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000)
+H018 nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000)
+OUTG 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000) 9.0000(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) nan(999.0000) 9.0000(999.0000) 9.0000(999.0000) nan(999.0000)
+
+TREE # 1: (((((((((((((((((13, 19), (6, (16, 34))), 32), 22), 35), (((33, (24, 1)), 5), 21)), 4), 12), 10), 14), 28), ((11, ((((((29, 31), (25, 8)), 20), 15), 3), 26)), 36)), 23), 18), (2, 7)), 30), (27, 9), 17); MP score: 38.00
+lnL(ntime: 34 np: 39): -161.595863 +0.000000
37..38 38..39 39..40 40..41 41..42 42..43 43..44 44..45 45..46 46..47 47..48 48..49 49..50 50..51 51..52 52..53 53..13 53..19 52..54 54..6 54..55 55..16 55..34 51..32 50..22 49..35 48..56 56..57 57..58 58..33 58..59 59..24 59..1 57..5 56..21 47..4 46..12 45..10 44..14 43..28 42..60 60..61 61..11 61..62 62..63 63..64 64..65 65..66 66..67 67..29 67..31 66..68 68..25 68..8 65..20 64..15 63..3 62..26 60..36 41..23 40..18 39..69 69..2 69..7 38..30 37..70 70..27 70..9 37..17
- 0.29506 0.29506 0.25204 0.21996 0.21996 0.19584 0.17361 0.12898 0.11393 0.11393 0.11393 0.10061 0.10061 0.07705 0.07705 0.07705 0.03142 0.05099 0.05099 0.07180 0.05119 0.03192 0.01484 0.19584 0.19584 0.13063 0.09238 0.06437 0.06437 0.06437 0.06437 0.02722 0.07328 0.11731 1.00000 0.21839 0.24112 0.21870 0.24735
+ 0.32909 0.32909 0.27647 0.23931 0.23931 0.21195 0.19110 0.14247 0.12649 0.12649 0.12649 0.11202 0.11202 0.08672 0.08672 0.08672 0.03516 0.05787 0.05787 0.07949 0.05674 0.03539 0.01646 0.21191 0.21191 0.14045 0.09884 0.06899 0.06899 0.06899 0.06899 0.02948 0.07806 0.13263 1.00000 0.21839 0.24112 0.21870 0.24735
-tree length = 4.53786
+tree length = 4.99889
(((((((((((((((((H010, H033), (H027, (H017, H014))), H011), H003), H018), (((H022, (H013, H019)), H034), H029)), H020), H001), H015), H028), H030), ((H006, ((((((H031, H005), (H032, H016)), H008), H024), H004), H025)), OUTG)), H035), H007), (H026, H023)), H012), (H021, H002), H009);
-(((((((((((((((((H010: 0.031418, H033: 0.031418): 0.045635, (H027: 0.050987, (H017: 0.050987, H014: 0.050987): 0.000000): 0.026065): 0.000000, H011: 0.077052): 0.000000, H003: 0.077053): 0.023554, H018: 0.100607): 0.000000, (((H022: 0.031920, (H013: 0.014845, H019: 0.014845): 0.017075): 0.019267, H034: 0.051187): 0.020614, H029: 0.071801): 0.028806): 0.013321, H020: 0.113928): 0.000000, H001: 0.113928): 0.000000, H015: 0.113928): 0.015048, H028: 0.128977): 0.044636, H030: 0.173613): 0.022224, ((H006: 0.195836, ((((((H031: 0.064366, H005: 0.064366): 0.000000, (H032: 0.027219, H016: 0.027219): 0.037147): 0.000000, H008: 0.064366): 0.000000, H024: 0.064366): 0.028012, H004: 0.092378): 0.038256, H025: 0.130634): 0.065201): 0.000000, OUTG: 0.195836): 0.000000): 0.024127, H035: 0.219963): 0.000000, H007: 0.219963): 0.032073, (H026: 0.073275, H023: 0.073275): 0.178761): 0.043019, H012: 0.295055): 0.000000, (H021: 0.117306, H002: 0.117306): 0.177750, H009: 0.295056);
+(((((((((((((((((H010: 0.035163, H033: 0.035163): 0.051559, (H027: 0.057874, (H017: 0.057874, H014: 0.057874): 0.000000): 0.028848): 0.000000, H011: 0.086722): 0.000000, H003: 0.086722): 0.025300, H018: 0.112022): 0.000000, (((H022: 0.035387, (H013: 0.016460, H019: 0.016460): 0.018928): 0.021351, H034: 0.056739): 0.022749, H029: 0.079488): 0.032534): 0.014469, H020: 0.126491): 0.000000, H001: 0.126491): 0.000000, H015: 0.126491): 0.015976, H028: 0.142467): 0.048638, H030: 0.191105): 0.020845, ((H006: 0.211909, ((((((H031: 0.068986, H005: 0.068986): 0.000000, (H032: 0.029484, H016: 0.029484): 0.039502): 0.000000, H008: 0.068986): 0.000000, H024: 0.068986): 0.029849, H004: 0.098835): 0.041617, H025: 0.140453): 0.071456): 0.000000, OUTG: 0.211909): 0.000041): 0.027363, H035: 0.239313): 0.000000, H007: 0.239313): 0.037161, (H026: 0.078062, H023: 0.078062): 0.198413): 0.052620, H012: 0.329094): 0.000000, (H021: 0.132628, H002: 0.132628): 0.196467, H009: 0.329095);
Detailed output identifying parameters
Parameters in the rate matrix (REV) (Yang 1994 J Mol Evol 39:105-111):
Rate parameters: 1.00000 0.21839 0.24112 0.21870 0.24735
-Base frequencies: 0.00000 0.49242 0.00000 0.50758
+Base frequencies: 0.00000 0.53889 0.00000 0.46111
Rate matrix Q, Average Ts/Tv = 0.0000
- -4.972327 3.982525 0.000000 0.989801
- 0.000000 -1.015385 0.000000 1.015385
- 0.000000 0.870993 -4.976058 4.105065
- 0.000000 0.985075 0.000000 -0.985075
+ -5.288293 4.383835 0.000000 0.904458
+ 0.000000 -0.927835 0.000000 0.927835
+ 0.000000 0.958761 -4.709878 3.751117
+ 0.000000 1.084337 0.000000 -1.084337
+check convergence..
diff --git a/test/paml/unrooted_absent/association/rst b/test/paml/unrooted_absent/association/rst
index 59865dec96e71f92c85e8e25ac2d576d449ed223..b01eb89167598019c30bbde099cd899a9b9994bc 100644
--- a/test/paml/unrooted_absent/association/rst
+++ b/test/paml/unrooted_absent/association/rst
@@ -8,14 +8,14 @@ TREE # 1
Ancestral reconstruction by BASEML.
-(((((((((((((((((H010: 0.031418, H033: 0.031418): 0.045635, (H027: 0.050987, (H017: 0.050987, H014: 0.050987): 0.000000): 0.026065): 0.000000, H011: 0.077052): 0.000000, H003: 0.077053): 0.023554, H018: 0.100607): 0.000000, (((H022: 0.031920, (H013: 0.014845, H019: 0.014845): 0.017075): 0.019267, H034: 0.051187): 0.020614, H029: 0.071801): 0.028806): 0.013321, H020: 0.113928): 0.000000, H001: 0.113928): 0.000000, H015: 0.113928): 0.015048, H028: 0.128977): 0.044636, H030: 0.173613): 0.022224, ((H006: 0.195836, ((((((H031: 0.064366, H005: 0.064366): 0.000000, (H032: 0.027219, H016: 0.027219): 0.037147): 0.000000, H008: 0.064366): 0.000000, H024: 0.064366): 0.028012, H004: 0.092378): 0.038256, H025: 0.130634): 0.065201): 0.000000, OUTG: 0.195836): 0.000000): 0.024127, H035: 0.219963): 0.000000, H007: 0.219963): 0.032073, (H026: 0.073275, H023: 0.073275): 0.178761): 0.043019, H012: 0.295055): 0.000000, (H021: 0.117306, H002: 0.117306): 0.177750, H009: 0.295056);
+(((((((((((((((((H010: 0.035163, H033: 0.035163): 0.051559, (H027: 0.057874, (H017: 0.057874, H014: 0.057874): 0.000000): 0.028848): 0.000000, H011: 0.086722): 0.000000, H003: 0.086722): 0.025300, H018: 0.112022): 0.000000, (((H022: 0.035387, (H013: 0.016460, H019: 0.016460): 0.018928): 0.021351, H034: 0.056739): 0.022749, H029: 0.079488): 0.032534): 0.014469, H020: 0.126491): 0.000000, H001: 0.126491): 0.000000, H015: 0.126491): 0.015976, H028: 0.142467): 0.048638, H030: 0.191105): 0.020845, ((H006: 0.211909, ((((((H031: 0.068986, H005: 0.068986): 0.000000, (H032: 0.029484, H016: 0.029484): 0.039502): 0.000000, H008: 0.068986): 0.000000, H024: 0.068986): 0.029849, H004: 0.098835): 0.041617, H025: 0.140453): 0.071456): 0.000000, OUTG: 0.211909): 0.000041): 0.027363, H035: 0.239313): 0.000000, H007: 0.239313): 0.037161, (H026: 0.078062, H023: 0.078062): 0.198413): 0.052620, H012: 0.329094): 0.000000, (H021: 0.132628, H002: 0.132628): 0.196467, H009: 0.329095);
(((((((((((((((((13, 19), (6, (16, 34))), 32), 22), 35), (((33, (24, 1)), 5), 21)), 4), 12), 10), 14), 28), ((11, ((((((29, 31), (25, 8)), 20), 15), 3), 26)), 36)), 23), 18), (2, 7)), 30), (27, 9), 17);
37..38 38..39 39..40 40..41 41..42 42..43 43..44 44..45 45..46 46..47 47..48 48..49 49..50 50..51 51..52 52..53 53..13 53..19 52..54 54..6 54..55 55..16 55..34 51..32 50..22 49..35 48..56 56..57 57..58 58..33 58..59 59..24 59..1 57..5 56..21 47..4 46..12 45..10 44..14 43..28 42..60 60..61 61..11 61..62 62..63 63..64 64..65 65..66 66..67 67..29 67..31 66..68 68..25 68..8 65..20 64..15 63..3 62..26 60..36 41..23 40..18 39..69 69..2 69..7 38..30 37..70 70..27 70..9 37..17
tree with node labels for Rod Page's TreeView
-(((((((((((((((((13_H010: 0.031418, 19_H033: 0.031418) 53 : 0.045635, (6_H027: 0.050987, (16_H017: 0.050987, 34_H014: 0.050987) 55 : 0.000000) 54 : 0.026065) 52 : 0.000000, 32_H011: 0.077052) 51 : 0.000000, 22_H003: 0.077053) 50 : 0.023554, 35_H018: 0.100607) 49 : 0.000000, (((33_H022: 0.031920, (24_H013: 0.014845, 1_H019: 0.014845) 59 : 0.017075) 58 : 0.019267, 5_H034: 0.051187) 57 : 0.020614, 21_H029: 0.071801) 56 : 0.028806) 48 : 0.013321, 4_H020: 0.113928) 47 : 0.000000, 12_H001: 0.113928) 46 : 0.000000, 10_H015: 0.113928) 45 : 0.015048, 14_H028: 0.128977) 44 : 0.044636, 28_H030: 0.173613) 43 : 0.022224, ((11_H006: 0.195836, ((((((29_H031: 0.064366, 31_H005: 0.064366) 67 : 0.000000, (25_H032: 0.027219, 8_H016: 0.027219) 68 : 0.037147) 66 : 0.000000, 20_H008: 0.064366) 65 : 0.000000, 15_H024: 0.064366) 64 : 0.028012, 3_H004: 0.092378) 63 : 0.038256, 26_H025: 0.130634) 62 : 0.065201) 61 : 0.000000, 36_OUTG: 0.195836) 60 : 0.000000) 42 : 0.024127, 23_H035: 0.219963) 41 : 0.000000, 18_H007: 0.219963) 40 : 0.032073, (2_H026: 0.073275, 7_H023: 0.073275) 69 : 0.178761) 39 : 0.043019, 30_H012: 0.295055) 38 : 0.000000, (27_H021: 0.117306, 9_H002: 0.117306) 70 : 0.177750, 17_H009: 0.295056) 37 ;
+(((((((((((((((((13_H010: 0.035163, 19_H033: 0.035163) 53 : 0.051559, (6_H027: 0.057874, (16_H017: 0.057874, 34_H014: 0.057874) 55 : 0.000000) 54 : 0.028848) 52 : 0.000000, 32_H011: 0.086722) 51 : 0.000000, 22_H003: 0.086722) 50 : 0.025300, 35_H018: 0.112022) 49 : 0.000000, (((33_H022: 0.035387, (24_H013: 0.016460, 1_H019: 0.016460) 59 : 0.018928) 58 : 0.021351, 5_H034: 0.056739) 57 : 0.022749, 21_H029: 0.079488) 56 : 0.032534) 48 : 0.014469, 4_H020: 0.126491) 47 : 0.000000, 12_H001: 0.126491) 46 : 0.000000, 10_H015: 0.126491) 45 : 0.015976, 14_H028: 0.142467) 44 : 0.048638, 28_H030: 0.191105) 43 : 0.020845, ((11_H006: 0.211909, ((((((29_H031: 0.068986, 31_H005: 0.068986) 67 : 0.000000, (25_H032: 0.029484, 8_H016: 0.029484) 68 : 0.039502) 66 : 0.000000, 20_H008: 0.068986) 65 : 0.000000, 15_H024: 0.068986) 64 : 0.029849, 3_H004: 0.098835) 63 : 0.041617, 26_H025: 0.140453) 62 : 0.071456) 61 : 0.000000, 36_OUTG: 0.211909) 60 : 0.000041) 42 : 0.027363, 23_H035: 0.239313) 41 : 0.000000, 18_H007: 0.239313) 40 : 0.037161, (2_H026: 0.078062, 7_H023: 0.078062) 69 : 0.198413) 39 : 0.052620, 30_H012: 0.329094) 38 : 0.000000, (27_H021: 0.132628, 9_H002: 0.132628) 70 : 0.196467, 17_H009: 0.329095) 37 ;
Nodes 37 to 70 are ancestral
@@ -26,17 +26,16 @@ Prob of best character at each node, listed by site
Site Freq Data:
- 1 1 GGGCGCCGCCCCCCGCCCGGGCCGGGGCGCGCGGCC: C(0.994) C(0.994) C(0.996) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(0.957) C(0.999) C(0.999) G(0.948) G(0.998) G(1.000) G(1.000) C(1.000) C(1.000) G(0.924) G(0.995) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.848) C(0.847)
- 2 1 CCCGCCCCCGGGCGCCCCCCCCCCCCCCCCCCCCCC: C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(0.995) C(0.938) G(0.745) G(0.774) G(0.774) G(0.774) C(0.996) C(0.996) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.995) C(0.995) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.998)
- 3 1 GCGGGCCGCGGGGGGCCGGGGGGGGGCGGCGGGCGG: C(0.937) C(0.937) C(0.760) G(0.973) G(0.973) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.995) C(0.995) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.992) C(0.993)
- 4 1 GCGGGCCCCGGGCGGCCCCGGCCGCGCGGCGCGCGG: C(0.994) C(0.994) C(0.981) C(0.926) C(0.926) G(0.997) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(0.998) G(0.998) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.997) G(0.997) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.981) C(0.999) C(0.997)
- 5 1 CGCGGGGCCGGGGGCGGGGCGCGCCGCGCGCGCGGG: G(0.979) G(0.979) G(0.997) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.995) G(0.944) C(0.974) C(1.000) G(1.000) G(1.000) G(0.826) C(0.948) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.999) C(0.930)
- 6 1 GCCCCGCGGCCCCCGCGCCGCCCGGCGCGGGCCCCC: G(0.755) G(0.755) C(0.908) C(0.997) C(0.997) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.999) C(1.000) C(0.998) C(0.964) G(0.988) C(1.000) C(1.000) C(0.976) C(0.869) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.996) G(0.980)
- 7 1 CGGCCCGGGCGCCCGCGGCGCCGCCGGGGGGCCCCG: G(0.999) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(0.923) C(0.962) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.964) G(0.999) G(0.998)
- 8 1 CGGCCCGGGCGCCGGCCGCGCCGCGGCGCGGCCCCG: G(0.952) G(0.952) G(0.994) G(1.000) G(1.000) G(1.000) G(0.976) G(0.705) C(0.999) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.999) G(0.816)
- 9 1 CGGCCCGGGGGCCCCCGGCGCCGCGGGCGGGCCCCG: G(0.999) G(0.999) G(1.000) G(1.000) G(1.000) G(0.998) C(0.737) C(0.988) C(0.999) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.998) G(0.998) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.999) G(0.998)
- 10 1 CCCGGGCCCCCCGCCCCCGCCCGGCCCCCCGCGCCC: C(0.999) C(0.999) C(0.999) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.979) C(0.999) C(0.999) C(0.920) G(0.894) G(0.932) G(0.918) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.998)
- 11 1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC: G(0.999) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.999) G(0.998)
+ 1 1 GGGCGCCGCCCCCCGCCCGGGCCGGGGCGCGCGGCC: C(0.989) C(0.989) C(0.993) C(0.999) C(0.999) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) C(0.948) C(0.998) C(0.998) G(0.948) G(0.997) G(1.000) G(1.000) C(0.999) C(0.999) G(0.924) G(0.995) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.824) C(0.824)
+ 2 1 CCCGCCCCCGGGCGCCCCCCCCCCCCCCCCCCCCCC: C(0.998) C(0.998) C(0.999) C(0.999) C(0.999) C(0.992) C(0.932) G(0.758) G(0.787) G(0.787) G(0.787) C(0.994) C(0.994) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.992) C(0.992) C(0.999) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.996)
+ 3 1 GCGGGCCGCGGGGGGCCGGGGGGGGGCGGCGGGCGG: C(0.908) C(0.908) C(0.703) G(0.975) G(0.975) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.992) C(0.992) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.990) C(0.989)
+ 4 1 GCGGGCCCCGGGCGGCCCCGGCCGCGCGGCGCGCGG: C(0.989) C(0.989) C(0.967) C(0.892) C(0.892) G(0.997) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(0.998) G(0.998) C(0.999) C(0.999) C(0.999) C(1.000) C(1.000) C(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.997) G(0.997) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.977) C(0.998) C(0.996)
+ 5 1 CGCGGGGCCGGGGGCGGGGCGCGCCGCGCGCGCGGG: G(0.974) G(0.974) G(0.996) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.994) G(0.943) C(0.969) C(1.000) G(1.000) G(1.000) G(0.826) C(0.942) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.999) C(0.916)
+ 6 1 GCCCCGCGGCCCCCGCGCCGCCCGGCGCGGGCCCCC: G(0.757) G(0.757) C(0.896) C(0.995) C(0.995) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.998) C(0.998) C(1.000) C(0.997) C(0.956) G(0.987) C(1.000) C(1.000) C(0.968) C(0.844) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) C(0.996) G(0.978)
+ 7 1 CGGCCCGGGCGCCCGCGGCGCCGCCGGGGGGCCCCG: G(0.999) G(0.999) G(0.999) G(1.000) G(1.000) G(1.000) G(0.932) C(0.956) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.964) G(0.999) G(0.997)
+ 8 1 CGGCCCGGGCGCCGGCCGCGCCGCGGCGCGGCCCCG: G(0.949) G(0.949) G(0.993) G(1.000) G(1.000) G(1.000) G(0.978) G(0.696) C(0.998) C(0.998) C(0.998) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.999) G(0.809)
+ 9 1 CGGCCCGGGGGCCCCCGGCGCCGCGGGCGGGCCCCG: G(0.999) G(0.999) G(0.999) G(1.000) G(1.000) G(0.997) C(0.670) C(0.982) C(0.998) C(0.998) C(0.998) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) G(0.997) G(0.997) G(0.999) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(1.000) G(0.999) G(0.997)
+ 10 1 CCCGGGCCCCCCGCCCCCGCCCGGCCCCCCGCGCCC: C(0.998) C(0.998) C(0.999) C(0.998) C(0.998) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.999) C(0.999) G(0.978) C(0.998) C(0.998) C(0.902) G(0.903) G(0.942) G(0.927) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(1.000) C(0.999) C(0.996)
Summary of changes along branches.
Check root for directions of change.
@@ -47,12 +46,12 @@ Branch 1: 37..38
Branch 2: 38..39
- 6 G 0.755 -> C 0.908
+ 6 G 0.757 -> C 0.896
Branch 3: 39..40
- 3 C 0.760 -> G 0.973
+ 3 C 0.703 -> G 0.975
Branch 4: 40..41
@@ -61,23 +60,23 @@ Branch 4: 40..41
Branch 5: 41..42
- 4 C 0.926 -> G 0.997
+ 4 C 0.892 -> G 0.997
Branch 6: 42..43
- 9 G 0.998 -> C 0.737
+ 9 G 0.997 -> C 0.670
Branch 7: 43..44
- 2 C 0.938 -> G 0.745
- 7 G 0.923 -> C 0.962
+ 2 C 0.932 -> G 0.758
+ 7 G 0.932 -> C 0.956
Branch 8: 44..45
- 8 G 0.705 -> C 0.999
+ 8 G 0.696 -> C 0.998
Branch 9: 45..46
@@ -90,7 +89,7 @@ Branch 10: 46..47
Branch 11: 47..48
- 2 G 0.774 -> C 0.996
+ 2 G 0.787 -> C 0.994
Branch 12: 48..49
@@ -99,7 +98,7 @@ Branch 12: 48..49
Branch 13: 49..50
- 4 G 0.998 -> C 1.000
+ 4 G 0.998 -> C 0.999
Branch 14: 50..51
@@ -112,7 +111,7 @@ Branch 15: 51..52
Branch 16: 52..53
- 10 C 1.000 -> G 0.979
+ 10 C 0.999 -> G 0.978
Branch 17: 53..13 (H010)
@@ -121,18 +120,18 @@ Branch 17: 53..13 (H010)
Branch 18: 53..19 (H033)
- 1 C 0.957 -> G
+ 1 C 0.948 -> G
Branch 19: 52..54
- 3 G 1.000 -> C 0.995
+ 3 G 1.000 -> C 0.992
Branch 20: 54..6 (H027)
- 6 C 0.999 -> G
- 10 C 0.999 -> G
+ 6 C 0.998 -> G
+ 10 C 0.998 -> G
Branch 21: 54..55
@@ -145,7 +144,7 @@ Branch 22: 55..16 (H017)
Branch 23: 55..34 (H014)
- 1 C 0.999 -> G
+ 1 C 0.998 -> G
Branch 24: 51..32 (H011)
@@ -168,12 +167,12 @@ Branch 27: 48..56
Branch 28: 56..57
- 10 C 0.920 -> G 0.894
+ 10 C 0.902 -> G 0.903
Branch 29: 57..58
- 5 G 0.944 -> C 0.974
+ 5 G 0.943 -> C 0.969
Branch 30: 58..33 (H022)
@@ -182,7 +181,7 @@ Branch 30: 58..33 (H022)
Branch 31: 58..59
- 6 C 0.964 -> G 0.988
+ 6 C 0.956 -> G 0.987
Branch 32: 59..24 (H013)
@@ -191,7 +190,7 @@ Branch 32: 59..24 (H013)
Branch 33: 59..1 (H019)
- 10 G 0.918 -> C
+ 10 G 0.927 -> C
Branch 34: 57..5 (H034)
@@ -213,7 +212,7 @@ Branch 37: 46..12 (H001)
Branch 38: 45..10 (H015)
- 9 C 0.999 -> G
+ 9 C 0.998 -> G
Branch 39: 44..14 (H028)
@@ -234,22 +233,22 @@ Branch 42: 60..61
Branch 43: 61..11 (H006)
- 2 C 0.995 -> G
+ 2 C 0.992 -> G
Branch 44: 61..62
- 1 C 1.000 -> G 0.924
+ 1 C 0.999 -> G 0.924
Branch 45: 62..63
- 5 G 0.826 -> C 0.948
+ 5 G 0.826 -> C 0.942
Branch 46: 63..64
- 6 C 0.869 -> G 1.000
+ 6 C 0.844 -> G 1.000
Branch 47: 64..65
@@ -276,7 +275,7 @@ Branch 51: 67..31 (H005)
Branch 52: 66..68
- 4 G 1.000 -> C 0.981
+ 4 G 1.000 -> C 0.977
Branch 53: 68..25 (H032)
@@ -307,12 +306,11 @@ Branch 58: 62..26 (H025)
Branch 59: 60..36 (OUTG)
- 11 G 1.000 -> C
Branch 60: 41..23 (H035)
- 10 C 0.999 -> G
+ 10 C 0.998 -> G
Branch 61: 40..18 (H007)
@@ -325,7 +323,7 @@ Branch 62: 39..69
Branch 63: 69..2 (H026)
- 1 C 0.848 -> G
+ 1 C 0.824 -> G
Branch 64: 69..7 (H023)
@@ -338,13 +336,13 @@ Branch 65: 38..30 (H012)
Branch 66: 37..70
- 5 G 0.979 -> C 0.930
+ 5 G 0.974 -> C 0.916
Branch 67: 70..27 (H021)
- 1 C 0.847 -> G
- 8 G 0.816 -> C
+ 1 C 0.824 -> G
+ 8 G 0.809 -> C
Branch 68: 70..9 (H002)
@@ -353,90 +351,90 @@ Branch 68: 70..9 (H002)
Branch 69: 37..17 (H009)
- 8 G 0.952 -> C
+ 8 G 0.949 -> C
List of extant and reconstructed sequences
-H019 GCGGCGCCCC G
-H026 GCCCGCGGGC G
-H004 GCGGCCGGGC G
-H020 CGGGGCCCCG G
-H034 GCGGGCCCCG G
-H027 CCCCGGCCCG G
-H023 CCCCGCGGGC G
-H016 GCGCCGGGGC G
-H002 CCCCCGGGGC G
-H015 CGGGGCCCGC G
-H006 CGGGGCGGGC G
-H001 CGGGGCCCCC G
-H010 CCGCGCCCCG G
-H028 CGGGGCCGCC G
-H024 GCGGCGGGCC G
-H017 CCCCGCCCCC G
-H009 CCCCGGGCGC G
-H007 CCGCGCGGGC G
-H033 GCGCGCCCCG G
-H008 GCGGCGGGGC G
-H029 GCGGGCCCCC G
-H003 CCGCCCCCCC G
-H035 CCGCGCGGGG G
-H013 GCGGCGCCCG G
-H032 GCGCCGCGGC G
-H025 GCGGGCGGGC G
-H021 GCCCCGGCGC G
-H030 CCGGGCGGCC G
-H031 GCGGCGGCGC G
-H012 CCCCGGGGGC G
-H005 GCGGCGGGGG G
-H011 CCGCGCCCCC G
-H022 GCGGCCCCCG G
-H014 GCCCGCCCCC G
-H018 CCGGGCCCCC G
-OUTG CCGGGCGGGC C
-node #37 CCCCGGGGGC G
-node #38 CCCCGGGGGC G
-node #39 CCCCGCGGGC G
-node #40 CCGCGCGGGC G
-node #41 CCGCGCGGGC G
-node #42 CCGGGCGGGC G
-node #43 CCGGGCGGCC G
-node #44 CGGGGCCGCC G
-node #45 CGGGGCCCCC G
-node #46 CGGGGCCCCC G
-node #47 CGGGGCCCCC G
-node #48 CCGGGCCCCC G
-node #49 CCGGGCCCCC G
-node #50 CCGCGCCCCC G
-node #51 CCGCGCCCCC G
-node #52 CCGCGCCCCC G
-node #53 CCGCGCCCCG G
-node #54 CCCCGCCCCC G
-node #55 CCCCGCCCCC G
-node #56 GCGGGCCCCC G
-node #57 GCGGGCCCCG G
-node #58 GCGGCCCCCG G
-node #59 GCGGCGCCCG G
-node #60 CCGGGCGGGC G
-node #61 CCGGGCGGGC G
-node #62 GCGGGCGGGC G
-node #63 GCGGCCGGGC G
-node #64 GCGGCGGGGC G
-node #65 GCGGCGGGGC G
-node #66 GCGGCGGGGC G
-node #67 GCGGCGGGGC G
-node #68 GCGCCGGGGC G
-node #69 CCCCGCGGGC G
-node #70 CCCCCGGGGC G
+H019 GCGGCGCCCC
+H026 GCCCGCGGGC
+H004 GCGGCCGGGC
+H020 CGGGGCCCCG
+H034 GCGGGCCCCG
+H027 CCCCGGCCCG
+H023 CCCCGCGGGC
+H016 GCGCCGGGGC
+H002 CCCCCGGGGC
+H015 CGGGGCCCGC
+H006 CGGGGCGGGC
+H001 CGGGGCCCCC
+H010 CCGCGCCCCG
+H028 CGGGGCCGCC
+H024 GCGGCGGGCC
+H017 CCCCGCCCCC
+H009 CCCCGGGCGC
+H007 CCGCGCGGGC
+H033 GCGCGCCCCG
+H008 GCGGCGGGGC
+H029 GCGGGCCCCC
+H003 CCGCCCCCCC
+H035 CCGCGCGGGG
+H013 GCGGCGCCCG
+H032 GCGCCGCGGC
+H025 GCGGGCGGGC
+H021 GCCCCGGCGC
+H030 CCGGGCGGCC
+H031 GCGGCGGCGC
+H012 CCCCGGGGGC
+H005 GCGGCGGGGG
+H011 CCGCGCCCCC
+H022 GCGGCCCCCG
+H014 GCCCGCCCCC
+H018 CCGGGCCCCC
+OUTG CCGGGCGGGC
+node #37 CCCCGGGGGC
+node #38 CCCCGGGGGC
+node #39 CCCCGCGGGC
+node #40 CCGCGCGGGC
+node #41 CCGCGCGGGC
+node #42 CCGGGCGGGC
+node #43 CCGGGCGGCC
+node #44 CGGGGCCGCC
+node #45 CGGGGCCCCC
+node #46 CGGGGCCCCC
+node #47 CGGGGCCCCC
+node #48 CCGGGCCCCC
+node #49 CCGGGCCCCC
+node #50 CCGCGCCCCC
+node #51 CCGCGCCCCC
+node #52 CCGCGCCCCC
+node #53 CCGCGCCCCG
+node #54 CCCCGCCCCC
+node #55 CCCCGCCCCC
+node #56 GCGGGCCCCC
+node #57 GCGGGCCCCG
+node #58 GCGGCCCCCG
+node #59 GCGGCGCCCG
+node #60 CCGGGCGGGC
+node #61 CCGGGCGGGC
+node #62 GCGGGCGGGC
+node #63 GCGGCCGGGC
+node #64 GCGGCGGGGC
+node #65 GCGGCGGGGC
+node #66 GCGGCGGGGC
+node #67 GCGGCGGGGC
+node #68 GCGCCGGGGC
+node #69 CCCCGCGGGC
+node #70 CCCCCGGGGC
Overall accuracy of the 34 ancestral sequences:
- 0.96430 0.96430 0.96673 0.99030 0.99030 0.99897 0.96110 0.94544 0.97923 0.97923 0.97923 0.99936 0.99936 0.99992 0.99992 0.99992 0.99410 0.99918 0.99918 0.98743 0.98479 0.98822 0.99134 0.99897 0.99897 0.97480 0.98281 1.00000 1.00000 1.00000 1.00000 0.99492 0.98441 0.95925
+ 0.95602 0.95602 0.95455 0.98584 0.98584 0.99846 0.95098 0.93915 0.97828 0.97828 0.97828 0.99902 0.99902 0.99985 0.99985 0.99985 0.99250 0.99861 0.99861 0.98433 0.98398 0.98669 0.99137 0.99846 0.99846 0.97139 0.97803 0.99999 0.99999 0.99999 0.99999 0.99410 0.97995 0.94975
for a site.
- 0.64910 0.64910 0.66689 0.89584 0.89584 0.98872 0.62168 0.49918 0.77199 0.77199 0.77199 0.99302 0.99302 0.99913 0.99913 0.99913 0.93600 0.99103 0.99103 0.86669 0.83945 0.87553 0.90582 0.98872 0.98872 0.74263 0.81876 0.99995 0.99995 0.99995 0.99995 0.94489 0.83161 0.61662
+ 0.61783 0.61783 0.59678 0.86222 0.86222 0.98464 0.56794 0.49507 0.78363 0.78363 0.78363 0.99023 0.99023 0.99850 0.99850 0.99850 0.92619 0.98612 0.98612 0.84934 0.84626 0.87260 0.91468 0.98469 0.98469 0.73579 0.79053 0.99994 0.99994 0.99994 0.99994 0.94183 0.80398 0.57972
for the sequence.
@@ -452,6 +450,5 @@ Counts of changes at sites
8 GC GC GC GC (4)
9 CG GC GC (3)
10 GC CG CG CG CG CG CG (7)
- 11 GC (1)
diff --git a/test/paml/unrooted_absent/association/rub b/test/paml/unrooted_absent/association/rub
index d9618a2378acf4ef2a7c634bd7dad824c1241f0c..aa2293e450e68f403ce2bc1b4dd7652d9187b939 100644
--- a/test/paml/unrooted_absent/association/rub
+++ b/test/paml/unrooted_absent/association/rub
@@ -2,39 +2,40 @@
TREE # 1
- 1 114.9094 191.446920 x: 0.80189 0.86355 1.00000 0.99305 0.89074 0.85919 0.70270 0.75174 0.74732 0.88922 0.84271 0.64707 0.57975 0.85413 0.86112 0.86851 0.77260 0.50918 0.42855 0.81496 0.71039 0.53319 0.76726 0.74305 0.74626 0.78847 0.82586 0.87508 0.51039 0.47093 0.87785 0.76907 0.53027 0.67918 1.00000 0.21839 0.24112 0.21870 0.24735
- 2 35.7482 180.282991 x: 0.60638 0.75031 0.91597 0.96161 0.91469 0.89863 0.78734 0.81227 0.84651 1.00000 0.98309 0.79766 0.70321 0.86828 0.92995 0.91683 0.74822 0.55330 0.44962 0.79545 0.71055 0.54220 0.73374 0.72619 0.74825 0.75977 0.79572 0.85004 0.56245 0.55610 0.89935 0.73261 0.48828 0.65383 1.00000 0.21839 0.24112 0.21870 0.24735
- 3 39.2096 178.600236 x: 0.55500 0.73939 0.91041 0.95773 0.93441 0.91006 0.78748 0.80006 0.84199 1.00000 1.00000 0.80649 0.71640 0.86085 0.94060 0.92616 0.74031 0.56059 0.45471 0.78710 0.70829 0.54275 0.72619 0.74652 0.77024 0.76556 0.79645 0.84572 0.58182 0.57891 0.90657 0.72393 0.47968 0.64540 1.00000 0.21839 0.24112 0.21870 0.24735
- 4 27.2762 174.769630 x: 0.42076 0.82026 0.94820 0.88667 0.99366 0.83049 0.80617 0.79557 0.86716 1.00000 1.00000 0.82582 0.78834 0.84595 1.00000 0.97842 0.70130 0.58890 0.48244 0.77342 0.70965 0.55395 0.69600 0.80490 0.83268 0.75295 0.77519 0.82405 0.64095 0.65367 0.93786 0.69273 0.46149 0.60485 1.00000 0.21839 0.24112 0.21870 0.24735
- 5 12.1266 174.514561 x: 0.41547 0.82949 0.94094 0.88163 1.00000 0.83355 0.80451 0.79395 0.86516 1.00000 1.00000 0.82666 0.79703 0.84356 1.00000 0.98686 0.69532 0.59082 0.48705 0.77445 0.71091 0.55602 0.69294 0.80542 0.83391 0.74780 0.77273 0.82394 0.64505 0.66005 0.94203 0.68995 0.46107 0.60029 1.00000 0.21839 0.24112 0.21870 0.24735
- 6 16.2354 174.212559 x: 0.41056 0.84010 0.93308 0.88836 1.00000 0.83485 0.80441 0.79469 0.86789 1.00000 1.00000 0.82655 0.80741 0.84140 1.00000 1.00000 0.68648 0.59233 0.49438 0.77292 0.71105 0.55773 0.68912 0.80901 0.83956 0.74903 0.77485 0.82371 0.65222 0.66976 0.94852 0.68631 0.45976 0.59471 1.00000 0.21839 0.24112 0.21870 0.24735
- 7 11.6723 173.108877 x: 0.31191 0.94409 0.84996 0.92905 1.00000 0.83020 0.87186 0.80407 0.87324 1.00000 1.00000 0.80127 0.82279 0.81341 1.00000 1.00000 0.60786 0.56252 0.56538 0.75462 0.70188 0.55931 0.67567 0.81739 0.86575 0.76618 0.78112 0.77786 0.66549 0.69793 1.00000 0.67450 0.46263 0.56482 1.00000 0.21839 0.24112 0.21870 0.24735
- 8 8.2869 172.274253 x: 0.31548 1.00000 0.80011 0.89267 1.00000 0.83067 0.92049 0.77063 0.85964 1.00000 1.00000 0.83363 0.82751 0.80298 1.00000 1.00000 0.54971 0.54329 0.62734 0.72647 0.68624 0.55278 0.66399 0.85017 0.91268 0.78895 0.77460 0.72294 0.68764 0.73296 1.00000 0.66016 0.45682 0.55097 1.00000 0.21839 0.24112 0.21870 0.24735
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+ 22 0.3483 161.605079 x: 0.33473 1.00000 0.83306 0.85747 1.00000 0.88272 0.90598 0.74121 0.88622 1.00000 1.00000 0.89070 1.00000 0.77790 1.00000 1.00000 0.40066 0.65497 1.00000 0.70599 0.70914 0.62374 0.46231 0.99700 1.00000 0.66154 0.70980 0.70015 1.00000 1.00000 1.00000 0.42349 0.27113 0.40129 1.00000 0.21839 0.24112 0.21870 0.24735
+ 23 0.2164 161.601734 x: 0.33263 1.00000 0.83778 0.86020 1.00000 0.88295 0.89778 0.74256 0.88806 1.00000 1.00000 0.88911 1.00000 0.77716 1.00000 1.00000 0.39894 0.66367 1.00000 0.70784 0.70826 0.62390 0.46498 0.99713 1.00000 0.65668 0.71212 0.69476 1.00000 1.00000 1.00000 0.42687 0.26937 0.40093 1.00000 0.21839 0.24112 0.21870 0.24735
+ 24 0.2547 161.599048 x: 0.33218 1.00000 0.83901 0.86028 1.00000 0.88274 0.90033 0.74474 0.88560 1.00000 1.00000 0.88820 1.00000 0.77240 1.00000 1.00000 0.39995 0.66884 1.00000 0.70958 0.70909 0.62370 0.46754 1.00000 1.00000 0.65626 0.71307 0.69319 1.00000 1.00000 1.00000 0.43006 0.27167 0.40137 1.00000 0.21839 0.24112 0.21870 0.24735
+ 26 0.7126 161.598561 x: 0.33268 1.00000 0.83978 0.86142 1.00000 0.88397 0.90086 0.74530 0.88624 1.00000 1.00000 0.88776 1.00000 0.77267 1.00000 1.00000 0.40013 0.66880 1.00000 0.70966 0.70929 0.62371 0.46749 0.99891 1.00000 0.65655 0.71289 0.69339 1.00000 1.00000 1.00000 0.43000 0.27200 0.40136 1.00000 0.21839 0.24112 0.21870 0.24735
+ 27 0.7472 161.597464 x: 0.33194 1.00000 0.84064 0.86304 1.00000 0.88568 0.90152 0.74600 0.88719 1.00000 1.00000 0.88680 1.00000 0.77307 1.00000 1.00000 0.40049 0.66868 1.00000 0.70978 0.70970 0.62373 0.46737 1.00000 1.00000 0.65704 0.71240 0.69375 1.00000 1.00000 1.00000 0.42986 0.27264 0.40130 1.00000 0.21839 0.24112 0.21870 0.24735
+ 28 0.8253 161.597007 x: 0.32978 1.00000 0.84094 0.86414 1.00000 0.88668 0.90184 0.74631 0.88785 1.00000 1.00000 0.88577 1.00000 0.77340 1.00000 1.00000 0.40089 0.66850 1.00000 0.70985 0.71015 0.62374 0.46722 0.99971 1.00000 0.65746 0.71172 0.69408 1.00000 1.00000 1.00000 0.42967 0.27340 0.40124 1.00000 0.21839 0.24112 0.21870 0.24735
+ 29 0.1950 161.596348 x: 0.32940 1.00000 0.84181 0.86664 1.00000 0.88469 0.90090 0.74495 0.88787 1.00000 1.00000 0.88460 1.00000 0.77453 1.00000 1.00000 0.40294 0.66763 1.00000 0.71009 0.71235 0.62373 0.46640 0.99971 1.00000 0.66005 0.70840 0.69599 1.00000 1.00000 1.00000 0.42875 0.27819 0.40192 1.00000 0.21839 0.24112 0.21870 0.24735
+ 30 0.2058 161.595960 x: 0.32936 1.00000 0.84031 0.86585 1.00000 0.88533 0.90205 0.74500 0.88838 1.00000 1.00000 0.88614 1.00000 0.77509 1.00000 1.00000 0.40486 0.66716 1.00000 0.71024 0.71414 0.62369 0.46563 0.99973 1.00000 0.66197 0.70495 0.69743 1.00000 1.00000 1.00000 0.42784 0.28225 0.40271 1.00000 0.21839 0.24112 0.21870 0.24735
+ 31 0.0738 161.595920 x: 0.32954 1.00000 0.83999 0.86551 1.00000 0.88584 0.90189 0.74501 0.88793 1.00000 1.00000 0.88563 1.00000 0.77457 1.00000 1.00000 0.40515 0.66720 1.00000 0.71003 0.71418 0.62362 0.46547 0.99973 1.00000 0.66245 0.70446 0.69773 1.00000 1.00000 1.00000 0.42769 0.28269 0.40292 1.00000 0.21839 0.24112 0.21870 0.24735
+ 32 0.0276 161.595905 x: 0.32949 1.00000 0.84007 0.86549 1.00000 0.88559 0.90190 0.74555 0.88800 1.00000 1.00000 0.88560 1.00000 0.77403 1.00000 1.00000 0.40538 0.66749 1.00000 0.70973 0.71391 0.62351 0.46530 0.99973 1.00000 0.66280 0.70403 0.69790 1.00000 1.00000 1.00000 0.42755 0.28262 0.40313 1.00000 0.21839 0.24112 0.21870 0.24735
+ 33 0.0218 161.595900 x: 0.32941 1.00000 0.84018 0.86558 1.00000 0.88567 0.90170 0.74561 0.88790 1.00000 1.00000 0.88583 1.00000 0.77397 1.00000 1.00000 0.40549 0.66765 1.00000 0.70961 0.71374 0.62347 0.46522 0.99974 1.00000 0.66298 0.70383 0.69798 1.00000 1.00000 1.00000 0.42748 0.28248 0.40324 1.00000 0.21839 0.24112 0.21870 0.24735
+ 34 0.0087 161.595894 x: 0.32940 1.00000 0.84019 0.86546 1.00000 0.88566 0.90166 0.74566 0.88785 1.00000 1.00000 0.88568 1.00000 0.77440 1.00000 1.00000 0.40564 0.66780 1.00000 0.70966 0.71353 0.62347 0.46510 0.99975 1.00000 0.66314 0.70348 0.69804 1.00000 1.00000 1.00000 0.42736 0.28211 0.40342 1.00000 0.21839 0.24112 0.21870 0.24735
+ 35 0.0045 161.595885 x: 0.32931 1.00000 0.84024 0.86546 1.00000 0.88564 0.90189 0.74525 0.88796 1.00000 1.00000 0.88564 1.00000 0.77416 1.00000 1.00000 0.40572 0.66758 1.00000 0.71013 0.71354 0.62364 0.46501 0.99976 1.00000 0.66336 0.70329 0.69822 1.00000 1.00000 1.00000 0.42725 0.28163 0.40352 1.00000 0.21839 0.24112 0.21870 0.24735
+ 36 0.0030 161.595868 x: 0.32920 1.00000 0.84011 0.86552 1.00000 0.88571 0.90146 0.74538 0.88817 1.00000 1.00000 0.88559 1.00000 0.77408 1.00000 1.00000 0.40554 0.66731 1.00000 0.70975 0.71374 0.62373 0.46508 0.99980 1.00000 0.66283 0.70342 0.69798 1.00000 1.00000 1.00000 0.42732 0.28210 0.40314 1.00000 0.21839 0.24112 0.21870 0.24735
+ 37 0.0092 161.595863 x: 0.32909 1.00000 0.84011 0.86559 1.00000 0.88566 0.90165 0.74549 0.88786 1.00000 1.00000 0.88561 1.00000 0.77415 1.00000 1.00000 0.40546 0.66735 1.00000 0.70958 0.71380 0.62369 0.46513 0.99981 1.00000 0.66280 0.70369 0.69799 1.00000 1.00000 1.00000 0.42739 0.28235 0.40301 1.00000 0.21839 0.24112 0.21870 0.24735
+ 38 0.0039 161.595863 x: 0.32909 1.00000 0.84011 0.86559 1.00000 0.88566 0.90165 0.74549 0.88786 1.00000 1.00000 0.88561 1.00000 0.77415 1.00000 1.00000 0.40546 0.66735 1.00000 0.70958 0.71380 0.62369 0.46513 0.99981 1.00000 0.66280 0.70369 0.69799 1.00000 1.00000 1.00000 0.42739 0.28235 0.40301 1.00000 0.21839 0.24112 0.21870 0.24735
+check convergence!
diff --git a/test/paup/ancestor_absent/association/1_caco.asso b/test/paup/ancestor_absent/association/1_caco.asso
index 3de1bee4f726625f126ffdab3a3dbeab048f5106..6ce818fba241fe975be65059b66cd34fa3d3ef0b 100644
--- a/test/paup/ancestor_absent/association/1_caco.asso
+++ b/test/paup/ancestor_absent/association/1_caco.asso
@@ -29,7 +29,7 @@
|----* H001 case/control:11/9
| Site: 1 Sens: 2-->1
| Site: 2 Sens: 2-->1
------* root+(20+(19)) case/control:102/74
+-----* 20+(19) case/control:102/74
|
| [0] ddl=3 chi2=1.41 p_value_chi2=0.704
| [1] ddl=5 chi2=3.37 p_value_chi2=0.643
diff --git a/test/paup/ancestor_absent/association/test.res.log b/test/paup/ancestor_absent/association/test.res.log
index 4bef63d42ed685d0d2b4d8547d31bdceb7f07ec3..48fd3923d9a10acbcbd639af06a44b27a88eadf9 100644
--- a/test/paup/ancestor_absent/association/test.res.log
+++ b/test/paup/ancestor_absent/association/test.res.log
@@ -1,7 +1,7 @@
P A U P *
Portable version 4.0b10 for Unix
-Tue Jan 10 20:41:04 2006
+Thu Jan 12 21:56:20 2006
-----------------------------NOTICE-----------------------------
This is a beta-test version. Please report any crashes,
diff --git a/test/paup/ancestor_absent/association/test.tree b/test/paup/ancestor_absent/association/test.tree
index 9b25032fddac3235a1ee7d453283fbadbcb5b96f..2398457015388e5f96c8f9a4297f7c51d1851baf 100644
--- a/test/paup/ancestor_absent/association/test.tree
+++ b/test/paup/ancestor_absent/association/test.tree
@@ -1,6 +1,6 @@
#NEXUS
-Begin trees; [Treefile saved Tue Jan 10 20:41:04 2006]
+Begin trees; [Treefile saved Thu Jan 12 21:56:20 2006]
[!
>Data file = /home/cbardel/recherche/logiciel/altree/test/paup/ancestor_absent/association/caco.paup
>Heuristic search settings:
@@ -26,7 +26,7 @@ Begin trees; [Treefile saved Tue Jan 10 20:41:04 2006]
> Total number of rearrangements tried = 69978
> Score of best tree(s) found = 20
> Number of trees retained = 89
-> Time used = <1 sec (CPU time = 0.09 sec)
+> Time used = 1 sec (CPU time = 0.09 sec)
]
tree PAUP_1 = [&R] (((((H002,(H008,H014),H009,H006),H007,H012,H011),H013),H001,(H003,H005)),H010);
tree PAUP_2 = [&R] (((((((H002,(H007,H012,H011),H009,H006),H008),H014),H013),H001),(H003,H005)),H010);
diff --git a/test/paup/ancestor_absent/localisation/test.res.log b/test/paup/ancestor_absent/localisation/test.res.log
index 79e2b98e6b26a291593f926a40c2e5b317f15d68..9edb861640c1242cd978313901da23a58c7a078b 100644
--- a/test/paup/ancestor_absent/localisation/test.res.log
+++ b/test/paup/ancestor_absent/localisation/test.res.log
@@ -1,7 +1,7 @@
P A U P *
Portable version 4.0b10 for Unix
-Tue Jan 10 21:16:27 2006
+Thu Jan 12 21:56:08 2006
-----------------------------NOTICE-----------------------------
This is a beta-test version. Please report any crashes,
diff --git a/test/paup/ancestor_absent/localisation/test.tree b/test/paup/ancestor_absent/localisation/test.tree
index c2d404c1a039b57326b43467e7e8882e6cb43aa3..df616854fe2ee5d3cacad6478c5b9f84c33f3a3c 100644
--- a/test/paup/ancestor_absent/localisation/test.tree
+++ b/test/paup/ancestor_absent/localisation/test.tree
@@ -1,6 +1,6 @@
#NEXUS
-Begin trees; [Treefile saved Tue Jan 10 21:16:27 2006]
+Begin trees; [Treefile saved Thu Jan 12 21:56:08 2006]
[!
>Data file = /home/cbardel/recherche/logiciel/altree/test/paup/ancestor_absent/localisation/et_caco.paup
>Heuristic search settings:
diff --git a/test/paup/ancestor_present/association/1_caco.asso b/test/paup/ancestor_present/association/1_caco.asso
index 3b7721dbb8d458479968c14dd832df57889edaff..0c5149d67fc2bba3df85fec5ff15f7069c4da70e 100644
--- a/test/paup/ancestor_present/association/1_caco.asso
+++ b/test/paup/ancestor_present/association/1_caco.asso
@@ -36,7 +36,7 @@
| | Site: 3 Sens: 2-->1
| \----* H005 case/control:7/7
| Site: 12 Sens: 2-->1
------* root+(22+(21)) case/control:200/200
+-----* 22+(21) case/control:200/200
|
| [0] ddl=4 chi2=9.33 p_value_chi2=0.0535
| [1] ddl=6 chi2=11.24 p_value_chi2=0.07
diff --git a/test/paup/ancestor_present/association/run_altree b/test/paup/ancestor_present/association/run_altree
index 7391fa9538412d748587d4624ac84371e2833435..b86bbe08173fbf66764112bb409a78d4188926e8 100755
--- a/test/paup/ancestor_present/association/run_altree
+++ b/test/paup/ancestor_present/association/run_altree
@@ -7,3 +7,10 @@ paup caco.paup
#test.res.log
../../../../altree -i test.res.log -j nb_cas_control.txt -a -t SNP \
-p paup -r 1 --tree-to-analyse 1 -o 1_caco.asso
+
+
+# To perform the association test without the permutation test (using
+# a theshold for the chi2)
+#../../../../altree -i test.res.log -j nb_cas_control.txt -a -t SNP \
+#-p paup --tree-to-analyse 1 --chi2-threshold 0.05 -r 0 \
+#-o 1_caco.asso
diff --git a/test/paup/ancestor_present/association/test.res.log b/test/paup/ancestor_present/association/test.res.log
index de8659fd8687d12c9bc3724497f735d500cff29f..fcd098f51164eff6d5f0538d63a2c87ba60e7aa3 100644
--- a/test/paup/ancestor_present/association/test.res.log
+++ b/test/paup/ancestor_present/association/test.res.log
@@ -1,7 +1,7 @@
P A U P *
Portable version 4.0b10 for Unix
-Tue Jan 10 20:44:21 2006
+Thu Jan 12 21:56:48 2006
-----------------------------NOTICE-----------------------------
This is a beta-test version. Please report any crashes,
diff --git a/test/paup/ancestor_present/association/test.tree b/test/paup/ancestor_present/association/test.tree
index c493aa48008be395d166a448d1d51526c691472b..7cb65888a943298c092812af99a50a117cdcd6c4 100644
--- a/test/paup/ancestor_present/association/test.tree
+++ b/test/paup/ancestor_present/association/test.tree
@@ -1,6 +1,6 @@
#NEXUS
-Begin trees; [Treefile saved Tue Jan 10 20:44:21 2006]
+Begin trees; [Treefile saved Thu Jan 12 21:56:48 2006]
[!
>Data file = /home/cbardel/recherche/logiciel/altree/test/paup/ancestor_present/association/caco.paup
>Heuristic search settings:
@@ -26,7 +26,7 @@ Begin trees; [Treefile saved Tue Jan 10 20:44:21 2006]
> Total number of rearrangements tried = 90130
> Score of best tree(s) found = 20
> Number of trees retained = 89
-> Time used = <1 sec (CPU time = 0.12 sec)
+> Time used = 1 sec (CPU time = 0.12 sec)
]
tree PAUP_1 = [&R] (((((H002,(H007,H012,H011),(H008,H006),H009),H014),H013),H001,(H003,H005),H000),H010);
tree PAUP_2 = [&R] ((((((H002,(H008,H006),H009),(H007,H012,H011)),H014),H013),H001,(H003,H005),H000),H010);
diff --git a/test/paup/ancestor_present/localisation/test.res.log b/test/paup/ancestor_present/localisation/test.res.log
index ab63669bf1bab2f39fff88220c3e3c3c18e5cf49..431274e793993eca760d8baa87acbea3dc07406d 100644
--- a/test/paup/ancestor_present/localisation/test.res.log
+++ b/test/paup/ancestor_present/localisation/test.res.log
@@ -1,7 +1,7 @@
P A U P *
Portable version 4.0b10 for Unix
-Tue Jan 10 21:20:05 2006
+Thu Jan 12 21:57:28 2006
-----------------------------NOTICE-----------------------------
This is a beta-test version. Please report any crashes,
diff --git a/test/paup/ancestor_present/localisation/test.tree b/test/paup/ancestor_present/localisation/test.tree
index 140fe171e6105bfb32bd96546bdf1ab851e567a7..ef4e2c44078d3c014448afff87806a64984d7ee4 100644
--- a/test/paup/ancestor_present/localisation/test.tree
+++ b/test/paup/ancestor_present/localisation/test.tree
@@ -1,6 +1,6 @@
#NEXUS
-Begin trees; [Treefile saved Tue Jan 10 21:20:05 2006]
+Begin trees; [Treefile saved Thu Jan 12 21:57:28 2006]
[!
>Data file = /home/cbardel/recherche/logiciel/altree/test/paup/ancestor_present/localisation/et_caco.paup
>Heuristic search settings:
diff --git a/test/paup/outgr_absent/association/test.res.log b/test/paup/outgr_absent/association/test.res.log
index b48bc5e0f82f1499d61314721eb8ee0b0799e8ac..4652e29b41fb13538dd8e8966683a4ff3c71db30 100644
--- a/test/paup/outgr_absent/association/test.res.log
+++ b/test/paup/outgr_absent/association/test.res.log
@@ -1,7 +1,7 @@
P A U P *
Portable version 4.0b10 for Unix
-Tue Jan 10 20:59:38 2006
+Thu Jan 12 21:57:50 2006
-----------------------------NOTICE-----------------------------
This is a beta-test version. Please report any crashes,
diff --git a/test/paup/outgr_absent/association/test.tree b/test/paup/outgr_absent/association/test.tree
index 447d739e32cbb44006e13563ea0ed1234fed90e5..899a0035b4d9f79e8a33258920c9f90013899e0b 100644
--- a/test/paup/outgr_absent/association/test.tree
+++ b/test/paup/outgr_absent/association/test.tree
@@ -1,6 +1,6 @@
#NEXUS
-Begin trees; [Treefile saved Tue Jan 10 20:59:38 2006]
+Begin trees; [Treefile saved Thu Jan 12 21:57:50 2006]
[!
>Data file = /home/cbardel/recherche/logiciel/altree/test/paup/outgr_absent/association/caco.paup
>Heuristic search settings: