Commit 51c4dc5b authored by oshahmir's avatar oshahmir
Browse files

removing unnecessary folders

parent e9c24b8d
[Buildset]
BuildItems=@Variant(\x00\x00\x00\t\x00\x00\x00\x00\x01\x00\x00\x00\x0b\x00\x00\x00\x00\x01\x00\x00\x00\x1c\x00f\x00a\x00s\x00t\x00c\x00o\x00d\x00e\x00m\x00l\x00.\x00g\x00i\x00t)
[CMake]
Build Directory Count=1
Current Build Directory Index=0
ProjectRootRelative=./
[CMake][CMake Build Directory 0]
Build Directory Path=file:///home/omid/Projects/fastcodeml.git/build
Build Type=Debug
CMake Binary=file:///usr/bin/cmake
Environment Profile=
Extra Arguments=
Install Directory=file:///usr/local
[Defines And Includes][Compiler]
Name=GCC
Path=gcc
Type=GCC
[Launch]
Launch Configurations=Launch Configuration 0
[Launch][Launch Configuration 0]
Configured Launch Modes=execute
Configured Launchers=nativeAppLauncher
Name=fast
Type=Native Application
[Launch][Launch Configuration 0][Data]
Arguments=-m 22 -bl -s 0 -nt 1 ../bad_cases/HBG010916-1.M0.009.nwk ../bad_cases/HBG010916-1.phy
Dependencies=@Variant(\x00\x00\x00\t\x00\x00\x00\x00\x01\x00\x00\x00\x0b\x00\x00\x00\x00\x02\x00\x00\x00\x1c\x00f\x00a\x00s\x00t\x00c\x00o\x00d\x00e\x00m\x00l\x00.\x00g\x00i\x00t\x00\x00\x00\x08\x00f\x00a\x00s\x00t)
Dependency Action=Build
EnvironmentGroup=
Executable=file:///home/omid/Projects/fastcodeml.git/
External Terminal=konsole --noclose --workdir %workdir -e %exe
Project Target=fastcodeml.git,fast
Use External Terminal=false
Working Directory=
isExecutable=false
[Project]
VersionControlSupport=kdevgit
(((((((((a0009:0.005122,a0005:0.005553):0.021588,(a0000:0.09922,a0003:0.056644):0.214725):0.010754,a0010:0.015175):0.074881,a0001:0.06595):0.010737,a0014:0.314409):0.007601,a0013:0.083805):0.264158,a0007:0.430493):0.340044,a0002:1.259416):0.66615,(((a0008:0.090909,a0011:0.107215):0.183011,(a0012:0.283332,a0004:0.851209):0.052773):0.459232,a0006:0.540195)#1:0.694423);
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(((((((a0000:0.150779,a0011:0.366606):0.020186,(a0008:0.189257,a0012:0.064304):0.491414):0.003135,(a0005:0.027918,(a0014:0.008119,a0002:0.002763):0.019253):0.07771):0.185033,a0009:0.275464):0.185673,a0003:0.29294):0.394691,a0013:1.474877)#1:0.414072,(((a0006:0.64944,a0001:0.369005):0.077098,(a0004:0.342883,a0010:0.114781):0.128282):0.442747,a0007:3.987982):0.466218);
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(((a0003:0.940287,(a0006:0.225433,((a0008:0.070547,(a0013:0.069575,((a0014:0.003074,a0001:0.01845):4e-06,a0005:0.005609):0.079689):0.000897):0.011044,(a0007:0.048967,a0009:0.066015):0.166874):0.139738)#1:0.1328):0.2447,a0012:0.90415):0.965229,((((a0010:0.146055,a0004:0.095622):0.272589,a0011:0.127978):0.109596,a0002:0.382271):0.498846,a0000:0.498494):1.032012);
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(((((((a0001:0.075468,a0005:0.085411):0.207804,(a0010:0.720769,a0006:0.020905):0.105001):0.012384,(a0000:0.142497,a0012:0.282057):0.018899):0.178792,a0009:0.443433)#1:0.714179,a0008:0.474661):0.143467,a0011:1.098262):0.162709,((a0007:0.348344,(a0003:0.324275,(a0013:0.17518,a0002:0.376901):0.198321):0.112915):0.242393,a0004:0.617143):0.19161);
This diff is collapsed.
CODONML (in paml version 4.8a, July 2014) ./bad_cases/HBG010916-1.phy
Model: several dN/dS ratios for branches for branches, omega = 1.000 fixed
Codon frequency model: F3x4
Site-class models: PositiveSelection
ns = 14 ls = 1038
Codon usage in sequences
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT 34 22 18 11 16 21 | Ser TCT 13 19 16 5 19 16 | Tyr TAT 20 20 22 4 11 21 | Cys TGT 12 11 9 2 10 8
TTC 16 15 20 29 19 18 | TCC 17 15 15 29 22 20 | TAC 13 14 17 30 22 19 | TGC 9 8 8 15 9 13
Leu TTA 10 1 1 0 2 2 | TCA 10 6 11 6 10 7 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 13 13 17 5 15 15 | TCG 3 2 4 7 1 7 | TAG 0 0 0 0 0 0 | Trp TGG 13 9 8 7 9 8
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT 12 7 13 4 8 7 | Pro CCT 12 14 13 6 12 6 | His CAT 12 11 8 1 9 10 | Arg CGT 9 11 6 4 10 7
CTC 22 21 15 20 22 17 | CCC 13 13 8 25 16 20 | CAC 8 6 9 16 9 9 | CGC 14 15 11 32 20 16
CTA 13 15 2 1 11 7 | CCA 19 16 15 1 15 7 | Gln CAA 5 6 10 0 5 3 | CGA 7 9 6 2 5 7
CTG 42 49 38 67 47 53 | CCG 1 2 5 11 3 8 | CAG 39 38 28 38 39 39 | CGG 13 13 4 13 13 6
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT 21 22 25 8 20 24 | Thr ACT 12 10 19 5 10 14 | Asn AAT 15 11 15 4 7 15 | Ser AGT 8 4 13 2 9 13
ATC 32 31 31 54 33 30 | ACC 21 22 14 29 23 20 | AAC 16 20 29 35 23 26 | AGC 19 23 13 22 15 12
ATA 12 3 9 0 3 8 | ACA 22 21 18 6 18 11 | Lys AAA 19 10 28 3 7 16 | Arg AGA 4 2 12 1 3 2
Met ATG 26 20 34 24 21 29 | ACG 3 6 5 18 7 11 | AAG 33 36 35 51 38 34 | AGG 4 6 7 2 7 5
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT 13 9 29 4 7 18 | Ala GCT 22 26 27 12 28 20 | Asp GAT 18 16 22 8 16 19 | Gly GGT 18 20 18 12 15 10
GTC 18 19 18 23 24 22 | GCC 32 46 30 47 41 42 | GAC 26 28 26 37 28 25 | GGC 28 30 14 42 30 26
GTA 12 7 8 2 8 14 | GCA 16 19 13 8 16 11 | Glu GAA 17 18 26 2 21 14 | GGA 12 12 25 4 11 17
GTG 52 65 48 71 62 53 | GCG 3 3 6 22 6 6 | GAG 45 55 54 69 51 56 | GGG 15 17 10 16 21 18
--------------------------------------------------------------------------------------------------------------------------------------
--------------------------------------------------------------------------------------------------------------------------------------
Phe TTT 12 20 16 15 9 20 | Ser TCT 8 15 18 14 11 16 | Tyr TAT 5 22 13 13 2 18 | Cys TGT 5 12 4 7 10 7
TTC 24 17 21 22 28 17 | TCC 29 18 16 19 28 19 | TAC 31 12 21 21 36 16 | TGC 14 8 17 14 9 11
Leu TTA 3 2 5 5 0 3 | TCA 4 6 6 5 2 4 | *** TAA 0 0 0 0 0 0 | *** TGA 0 0 0 0 0 0
TTG 8 17 9 10 6 11 | TCG 10 2 2 5 8 3 | TAG 0 0 0 0 0 0 | Trp TGG 6 8 9 9 8 9
--------------------------------------------------------------------------------------------------------------------------------------
Leu CTT 5 11 9 9 4 13 | Pro CCT 11 20 7 9 8 13 | His CAT 6 7 8 7 4 8 | Arg CGT 4 8 11 9 4 14
CTC 17 17 23 22 21 17 | CCC 13 11 18 16 19 13 | CAC 15 13 12 12 12 11 | CGC 15 14 10 12 12 15
CTA 1 12 11 6 1 10 | CCA 6 11 15 17 5 16 | Gln CAA 4 12 8 7 1 6 | CGA 5 16 12 7 3 5
CTG 61 47 51 55 62 53 | CCG 13 2 3 2 7 3 | CAG 35 28 34 34 38 37 | CGG 8 10 16 22 11 17
--------------------------------------------------------------------------------------------------------------------------------------
Ile ATT 3 24 25 25 5 21 | Thr ACT 7 24 13 10 3 12 | Asn AAT 1 13 10 10 2 9 | Ser AGT 6 15 11 10 3 9
ATC 55 26 30 30 54 30 | ACC 26 12 19 23 34 18 | AAC 42 17 21 21 42 21 | AGC 20 13 16 17 19 19
ATA 2 6 3 4 5 6 | ACA 7 20 19 19 4 20 | Lys AAA 20 10 10 11 20 9 | Arg AGA 2 3 3 4 4 1
Met ATG 29 22 20 19 30 20 | ACG 14 3 7 7 19 9 | AAG 40 35 36 37 42 36 | AGG 13 7 3 2 10 7
--------------------------------------------------------------------------------------------------------------------------------------
Val GTT 11 16 10 11 12 9 | Ala GCT 26 35 30 34 12 34 | Asp GAT 11 22 13 14 10 18 | Gly GGT 11 20 23 18 14 14
GTC 29 21 20 20 28 21 | GCC 37 29 44 41 41 39 | GAC 39 23 32 31 42 26 | GGC 32 25 29 31 25 35
GTA 6 20 18 15 6 7 | GCA 4 26 14 14 7 15 | Glu GAA 7 29 19 17 7 22 | GGA 17 16 10 9 14 11
GTG 56 41 49 52 56 61 | GCG 12 3 5 1 18 5 | GAG 63 45 54 55 65 50 | GGG 12 19 17 21 16 19
--------------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------
Phe TTT 19 16 | Ser TCT 9 16 | Tyr TAT 10 17 | Cys TGT 7 7
TTC 18 22 | TCC 29 17 | TAC 29 23 | TGC 9 10
Leu TTA 0 1 | TCA 3 8 | *** TAA 0 0 | *** TGA 0 0
TTG 13 8 | TCG 9 9 | TAG 0 0 | Trp TGG 8 7
----------------------------------------------------------------------
Leu CTT 5 4 | Pro CCT 9 10 | His CAT 2 5 | Arg CGT 5 5
CTC 27 23 | CCC 18 12 | CAC 15 12 | CGC 15 12
CTA 2 2 | CCA 8 12 | Gln CAA 4 5 | CGA 6 5
CTG 47 55 | CCG 5 7 | CAG 36 34 | CGG 3 3
----------------------------------------------------------------------
Ile ATT 9 15 | Thr ACT 9 14 | Asn AAT 6 7 | Ser AGT 8 11
ATC 55 42 | ACC 21 20 | AAC 38 36 | AGC 14 14
ATA 2 9 | ACA 13 10 | Lys AAA 16 21 | Arg AGA 3 5
Met ATG 27 30 | ACG 12 15 | AAG 44 41 | AGG 12 11
----------------------------------------------------------------------
Val GTT 13 19 | Ala GCT 11 20 | Asp GAT 10 14 | Gly GGT 6 20
GTC 31 27 | GCC 42 34 | GAC 43 36 | GGC 37 22
GTA 4 6 | GCA 7 15 | Glu GAA 19 17 | GGA 13 15
GTG 55 47 | GCG 19 6 | GAG 57 59 | GGG 12 13
----------------------------------------------------------------------
Codon position x base (3x4) table for each sequence.
#1: a0010
position 1: T:0.17630 C:0.23218 A:0.25723 G:0.33430
position 2: T:0.33526 C:0.21098 A:0.27553 G:0.17823
position 3: T:0.24181 C:0.29287 A:0.17148 G:0.29383
Average T:0.25112 C:0.24534 A:0.23475 G:0.26879
#2: a0006
position 1: T:0.14933 C:0.23699 A:0.23796 G:0.37572
position 2: T:0.30732 C:0.23121 A:0.27842 G:0.18304
position 3: T:0.22447 C:0.31407 A:0.13969 G:0.32177
Average T:0.22704 C:0.26076 A:0.21869 G:0.29351
#3: a0004
position 1: T:0.15992 C:0.18401 A:0.29576 G:0.36031
position 2: T:0.31407 C:0.21098 A:0.31696 G:0.15800
position 3: T:0.26301 C:0.26782 A:0.17726 G:0.29191
Average T:0.24566 C:0.22094 A:0.26333 G:0.27007
#4: a0008
position 1: T:0.14507 C:0.23308 A:0.25532 G:0.36654
position 2: T:0.31238 C:0.22921 A:0.28820 G:0.17021
position 3: T:0.08897 C:0.46905 A:0.03482 G:0.40716
Average T:0.18214 C:0.31044 A:0.19278 G:0.31464
#5: a0012
position 1: T:0.15896 C:0.23507 A:0.23507 G:0.37091
position 2: T:0.30636 C:0.23796 A:0.27553 G:0.18015
position 3: T:0.19942 C:0.34297 A:0.13006 G:0.32755
Average T:0.22158 C:0.27200 A:0.21355 G:0.29287
#6: a0011
position 1: T:0.16859 C:0.21387 A:0.26012 G:0.35742
position 2: T:0.32563 C:0.21773 A:0.29480 G:0.16185
position 3: T:0.22062 C:0.32274 A:0.12139 G:0.33526
Average T:0.23828 C:0.25145 A:0.22543 G:0.28484
#7: a0002
position 1: T:0.15318 C:0.21098 A:0.27649 G:0.35934
position 2: T:0.31021 C:0.21869 A:0.30732 G:0.16378
position 3: T:0.12717 C:0.42197 A:0.08478 G:0.36609
Average T:0.19685 C:0.28388 A:0.22286 G:0.29640
#8: a0009
position 1: T:0.15318 C:0.23025 A:0.24085 G:0.37572
position 2: T:0.30732 C:0.22832 A:0.27746 G:0.18690
position 3: T:0.27360 C:0.26590 A:0.18208 G:0.27842
Average T:0.24470 C:0.24149 A:0.23346 G:0.28035
#9: a0005
position 1: T:0.15125 C:0.23892 A:0.23699 G:0.37283
position 2: T:0.30829 C:0.22736 A:0.28035 G:0.18401
position 3: T:0.21291 C:0.33622 A:0.14740 G:0.30347
Average T:0.22415 C:0.26750 A:0.22158 G:0.28677
#10: a0001
position 1: T:0.15318 C:0.23699 A:0.23988 G:0.36994
position 2: T:0.30829 C:0.22736 A:0.27938 G:0.18497
position 3: T:0.20713 C:0.33911 A:0.13487 G:0.31888
Average T:0.22286 C:0.26782 A:0.21805 G:0.29127
#11: a0007
position 1: T:0.15125 C:0.20424 A:0.28516 G:0.35934
position 2: T:0.31503 C:0.21773 A:0.31118 G:0.15607
position 3: T:0.10886 C:0.43353 A:0.07611 G:0.38150
Average T:0.19171 C:0.28516 A:0.22415 G:0.29897
#12: a0000
position 1: T:0.14836 C:0.24181 A:0.23796 G:0.37187
position 2: T:0.30732 C:0.23025 A:0.27649 G:0.18593
position 3: T:0.22640 C:0.31599 A:0.13006 G:0.32755
Average T:0.22736 C:0.26268 A:0.21484 G:0.29512
#13: a0003
position 1: T:0.15703 C:0.19942 A:0.27842 G:0.36513
position 2: T:0.31503 C:0.21580 A:0.31696 G:0.15222
position 3: T:0.13295 C:0.42486 A:0.09634 G:0.34586
Average T:0.20167 C:0.28003 A:0.23057 G:0.28773
#14: a0013
position 1: T:0.15511 C:0.19846 A:0.28998 G:0.35645
position 2: T:0.31407 C:0.21676 A:0.31503 G:0.15414
position 3: T:0.19268 C:0.34875 A:0.12620 G:0.33237
Average T:0.22062 C:0.25466 A:0.24374 G:0.28099
Sums of codon usage counts
------------------------------------------------------------------------------
Phe F TTT 249 | Ser S TCT 195 | Tyr Y TAT 198 | Cys C TGT 111
TTC 286 | TCC 293 | TAC 304 | TGC 154
Leu L TTA 35 | TCA 88 | *** * TAA 0 | *** * TGA 0
TTG 160 | TCG 72 | TAG 0 | Trp W TGG 118
------------------------------------------------------------------------------
Leu L CTT 111 | Pro P CCT 150 | His H CAT 98 | Arg R CGT 107
CTC 284 | CCC 215 | CAC 159 | CGC 213
CTA 94 | CCA 163 | Gln Q CAA 76 | CGA 95
CTG 727 | CCG 72 | CAG 497 | CGG 152
------------------------------------------------------------------------------
Ile I ATT 247 | Thr T ACT 162 | Asn N AAT 125 | Ser S AGT 122
ATC 533 | ACC 302 | AAC 387 | AGC 236
ATA 72 | ACA 208 | Lys K AAA 200 | Arg R AGA 49
Met M ATG 351 | ACG 136 | AAG 538 | AGG 96
------------------------------------------------------------------------------
Val V GTT 181 | Ala A GCT 337 | Asp D GAT 211 | Gly G GGT 219
GTC 321 | GCC 545 | GAC 442 | GGC 406
GTA 133 | GCA 185 | Glu E GAA 235 | GGA 186
GTG 768 | GCG 115 | GAG 778 | GGG 226
------------------------------------------------------------------------------
(Ambiguity data are not used in the counts.)
Codon position x base (3x4) table, overall
position 1: T:0.15577 C:0.22116 A:0.25909 G:0.36399
position 2: T:0.31333 C:0.22288 A:0.29240 G:0.17139
position 3: T:0.19431 C:0.34967 A:0.12521 G:0.33081
Average T:0.22114 C:0.26457 A:0.22556 G:0.28873
Nei & Gojobori 1986. dN/dS (dN, dS)
(Pairwise deletion)
(Note: This matrix is not used in later ML. analysis.
Use runmode = -2 for ML pairwise comparison.)
a0010
a0006 0.5463 (0.1461 0.2674)
a0004 0.1023 (0.2590 2.5320) 0.0593 (0.1205 2.0328)
a0008 0.1486 (0.2298 1.5464) 0.0765 (0.0884 1.1548) 0.0427 (0.0880 2.0622)
a0012 0.2550 (0.1756 0.6884) 0.0529 (0.0250 0.4720) 0.0653 (0.1436 2.1991) 0.0983 (0.1114 1.1336)
a0011 0.1541 (0.2982 1.9356) 0.0865 (0.1468 1.6977) 0.0608 (0.1349 2.2175) 0.0903 (0.1120 1.2412) 0.0979 (0.1708 1.7453)
a0002 0.1358 (0.2905 2.1391) 0.0885 (0.1452 1.6418) 0.0465 (0.0889 1.9101) 0.1353 (0.1196 0.8841) 0.1061 (0.1680 1.5843) 0.0983 (0.1640 1.6677)
a0009 0.1350 (0.1659 1.2292) 0.0201 (0.0208 1.0320) 0.0588 (0.1206 2.0516) 0.0472 (0.0915 1.9382) 0.0319 (0.0416 1.3058) 0.0703 (0.1405 1.9997)-1.0000 (0.1375 -1.0000)
a0005 0.2387 (0.1569 0.6572) 0.0252 (0.0135 0.5342) 0.0637 (0.1243 1.9514) 0.0765 (0.0922 1.2053) 0.0486 (0.0343 0.7052) 0.0670 (0.1437 2.1447) 0.0902 (0.1463 1.6214) 0.0177 (0.0241 1.3586)
a0001 0.2292 (0.1566 0.6834) 0.0268 (0.0141 0.5274) 0.0642 (0.1245 1.9408) 0.0848 (0.0958 1.1298) 0.0517 (0.0344 0.6657) 0.0748 (0.1461 1.9522) 0.0977 (0.1459 1.4936) 0.0193 (0.0254 1.3190) 0.0247 (0.0050 0.2013)
a0007 0.1406 (0.2647 1.8828) 0.0732 (0.1198 1.6373) 0.0319 (0.0570 1.7889) 0.1125 (0.0915 0.8137) 0.1015 (0.1407 1.3860) 0.0934 (0.1346 1.4423) 0.0799 (0.0635 0.7950) 0.0352 (0.1193 3.3922) 0.0742 (0.1208 1.6283) 0.0790 (0.1227 1.5536)
a0000 0.2668 (0.1515 0.5676) 0.0170 (0.0067 0.3944) 0.0621 (0.1212 1.9519) 0.0796 (0.0886 1.1124) 0.0583 (0.0275 0.4727) 0.0848 (0.1445 1.7040) 0.0881 (0.1423 1.6154) 0.0179 (0.0213 1.1933) 0.0259 (0.0146 0.5620) 0.0245 (0.0135 0.5496) 0.0807 (0.1174 1.4549)
a0003 0.1382 (0.2642 1.9113) 0.0795 (0.1218 1.5321) 0.0300 (0.0603 2.0140) 0.0958 (0.0932 0.9735) 0.0980 (0.1447 1.4763) 0.0872 (0.1394 1.5988) 0.0768 (0.0638 0.8307) 0.0554 (0.1222 2.2038) 0.0791 (0.1241 1.5693) 0.0807 (0.1266 1.5683) 0.0501 (0.0396 0.7911) 0.0822 (0.1225 1.4907)
a0013 0.1294 (0.2690 2.0790) 0.0719 (0.1242 1.7271) 0.0338 (0.0597 1.7675) 0.0706 (0.0930 1.3176) 0.0852 (0.1448 1.6992) 0.0723 (0.1362 1.8829) 0.0785 (0.0430 0.5483) 0.0453 (0.1182 2.6118) 0.0713 (0.1259 1.7655) 0.0775 (0.1282 1.6543) 0.0344 (0.0340 0.9889) 0.0703 (0.1229 1.7491) 0.0384 (0.0326 0.8489)
NOTE: -1 means that NG86 is inapplicable.
TREE # 1: (((((((10, 9), (1, 2)), (12, 5)), 8), 4), 6), ((11, (13, (14, 7))), 3)); MP score: -1
This is a rooted tree. Please check!
lnL(ntime: 0 np: 4): -21453.788139 +0.000000
2.192281 0.947748 0.033195 0.048787
tree length = 7.47378
(((((((10: 0.075468, 9: 0.085411): 0.207804, (1: 0.720769, 2: 0.020905): 0.105001): 0.012384, (12: 0.142497, 5: 0.282057): 0.018899): 0.178792, 8: 0.443433): 0.714179, 4: 0.474661): 0.143467, 6: 1.098262): 0.162709, ((11: 0.348344, (13: 0.324275, (14: 0.175180, 7: 0.376901): 0.198321): 0.112915): 0.242393, 3: 0.617143): 0.191610);
(((((((a0001: 0.075468, a0005: 0.085411): 0.207804, (a0010: 0.720769, a0006: 0.020905): 0.105001): 0.012384, (a0000: 0.142497, a0012: 0.282057): 0.018899): 0.178792, a0009: 0.443433): 0.714179, a0008: 0.474661): 0.143467, a0011: 1.098262): 0.162709, ((a0007: 0.348344, (a0003: 0.324275, (a0013: 0.175180, a0002: 0.376901): 0.198321): 0.112915): 0.242393, a0004: 0.617143): 0.191610);
Detailed output identifying parameters
kappa (ts/tv) = 2.19228
dN/dS (w) for site classes (K=4)
site class 0 1 2a 2b
proportion 0.94775 0.03319 0.01841 0.00064
background w 0.04879 1.00000 0.04879 1.00000
foreground w 0.04879 1.00000 1.00000 1.00000
Time used: 3:17
This diff is collapsed.
This diff is collapsed.
Branch(es): 10 19
LnL0: -21435.831385499266617
Branch lengths: 0.3543190 0.2423930 0.3483440 0.1129150 0.3242750 0.1983210 0.1751800 0.3769010
0.6171430 0.1434670 0.7141790 0.1787920 0.0123840 0.2078040 0.0754680 0.0854110
0.1050010 0.7207690 0.0209050 0.0188990 0.1424970 0.2820570 0.4434330 0.4746610
1.0982620
p0: 0.9171740 p1: 0.0298918 p2a: 0.0512635 p2b: 0.0016707
w0: 0.0472422 k: 2.1882731
LnL1: -21421.309962513714709
Branch lengths: 0.3543190 0.2423930 0.3483440 0.1129150 0.3242750 0.1983210 0.1751800 0.3769010
0.6171430 0.1434670 0.7141790 0.1787920 0.0123840 0.2078040 0.0754680 0.0854110
0.1050010 0.7207690 0.0209050 0.0188990 0.1424970 0.2820570 0.4434330 0.4746610
1.0982620
p0: 0.9320864 p1: 0.0291389 p2a: 0.0375993 p2b: 0.0011754
w0: 0.0484549 k: 2.1939564 w2: 6.7923102
Positive Selection Sites for branch(es): 10 19 Site: 2 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 6 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 11 Prob: 0.994976
Positive Selection Sites for branch(es): 10 19 Site: 13 Prob: 0.994965
Positive Selection Sites for branch(es): 10 19 Site: 16 Prob: 0.997751
Positive Selection Sites for branch(es): 10 19 Site: 18 Prob: 0.999430
Positive Selection Sites for branch(es): 10 19 Site: 32 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 39 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 70 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 74 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 100 Prob: 0.999395
Positive Selection Sites for branch(es): 10 19 Site: 110 Prob: 0.839957
Positive Selection Sites for branch(es): 10 19 Site: 112 Prob: 0.999732
Positive Selection Sites for branch(es): 10 19 Site: 114 Prob: 0.999965
Positive Selection Sites for branch(es): 10 19 Site: 118 Prob: 0.989097
Positive Selection Sites for branch(es): 10 19 Site: 121 Prob: 0.912637
Positive Selection Sites for branch(es): 10 19 Site: 124 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 138 Prob: 0.999800
Positive Selection Sites for branch(es): 10 19 Site: 139 Prob: 0.985332
Positive Selection Sites for branch(es): 10 19 Site: 147 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 165 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 166 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 170 Prob: 0.999563
Positive Selection Sites for branch(es): 10 19 Site: 171 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 173 Prob: 0.974745
Positive Selection Sites for branch(es): 10 19 Site: 194 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 197 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 199 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 202 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 203 Prob: 0.962114
Positive Selection Sites for branch(es): 10 19 Site: 214 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 252 Prob: 0.621910
Positive Selection Sites for branch(es): 10 19 Site: 279 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 292 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 296 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 298 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 301 Prob: 0.988906
Positive Selection Sites for branch(es): 10 19 Site: 303 Prob: 0.997505
Positive Selection Sites for branch(es): 10 19 Site: 317 Prob: 0.999990
Positive Selection Sites for branch(es): 10 19 Site: 326 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 359 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 362 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 364 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 404 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 418 Prob: 0.966054
Positive Selection Sites for branch(es): 10 19 Site: 422 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 426 Prob: 0.999997
Positive Selection Sites for branch(es): 10 19 Site: 427 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 429 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 430 Prob: 0.991818
Positive Selection Sites for branch(es): 10 19 Site: 431 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 434 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 452 Prob: 0.999895
Positive Selection Sites for branch(es): 10 19 Site: 460 Prob: 0.840190
Positive Selection Sites for branch(es): 10 19 Site: 483 Prob: 0.999248
Positive Selection Sites for branch(es): 10 19 Site: 493 Prob: 0.987467
Positive Selection Sites for branch(es): 10 19 Site: 503 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 504 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 511 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 513 Prob: 0.999548
Positive Selection Sites for branch(es): 10 19 Site: 526 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 527 Prob: 0.908478
Positive Selection Sites for branch(es): 10 19 Site: 546 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 547 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 554 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 587 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 595 Prob: 0.995378
Positive Selection Sites for branch(es): 10 19 Site: 596 Prob: 0.888148
Positive Selection Sites for branch(es): 10 19 Site: 616 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 622 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 639 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 643 Prob: 0.999947
Positive Selection Sites for branch(es): 10 19 Site: 665 Prob: 0.999878
Positive Selection Sites for branch(es): 10 19 Site: 674 Prob: 0.995159
Positive Selection Sites for branch(es): 10 19 Site: 680 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 688 Prob: 0.999924
Positive Selection Sites for branch(es): 10 19 Site: 693 Prob: 0.990301
Positive Selection Sites for branch(es): 10 19 Site: 694 Prob: 0.997580
Positive Selection Sites for branch(es): 10 19 Site: 699 Prob: 0.968681
Positive Selection Sites for branch(es): 10 19 Site: 703 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 707 Prob: 0.998398
Positive Selection Sites for branch(es): 10 19 Site: 708 Prob: 0.514372
Positive Selection Sites for branch(es): 10 19 Site: 713 Prob: 0.770127
Positive Selection Sites for branch(es): 10 19 Site: 715 Prob: 0.994547
Positive Selection Sites for branch(es): 10 19 Site: 745 Prob: 0.999922
Positive Selection Sites for branch(es): 10 19 Site: 750 Prob: 0.999958
Positive Selection Sites for branch(es): 10 19 Site: 752 Prob: 0.981884
Positive Selection Sites for branch(es): 10 19 Site: 756 Prob: 0.998924
Positive Selection Sites for branch(es): 10 19 Site: 769 Prob: 0.999976
Positive Selection Sites for branch(es): 10 19 Site: 772 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 792 Prob: 0.974949
Positive Selection Sites for branch(es): 10 19 Site: 799 Prob: 0.986104
Positive Selection Sites for branch(es): 10 19 Site: 803 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 804 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 824 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 826 Prob: 0.999964
Positive Selection Sites for branch(es): 10 19 Site: 830 Prob: 0.999593
Positive Selection Sites for branch(es): 10 19 Site: 840 Prob: 0.988110
Positive Selection Sites for branch(es): 10 19 Site: 865 Prob: 0.991506
Positive Selection Sites for branch(es): 10 19 Site: 867 Prob: 0.962281
Positive Selection Sites for branch(es): 10 19 Site: 876 Prob: 0.997681
Positive Selection Sites for branch(es): 10 19 Site: 882 Prob: 0.932576
Positive Selection Sites for branch(es): 10 19 Site: 883 Prob: 0.998854
Positive Selection Sites for branch(es): 10 19 Site: 886 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 895 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 928 Prob: 0.826382
Positive Selection Sites for branch(es): 10 19 Site: 934 Prob: 0.999144
Positive Selection Sites for branch(es): 10 19 Site: 958 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 975 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 1004 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 1005 Prob: 1.000000
Positive Selection Sites for branch(es): 10 19 Site: 1009 Prob: 0.595517
Positive Selection Sites for branch(es): 10 19 Site: 1012 Prob: 0.998376
Positive Selection Sites for branch(es): 10 19 Site: 1017 Prob: 0.999983
Positive Selection Sites for branch(es): 10 19 Site: 1025 Prob: 0.999941
Positive Selection Sites for branch(es): 10 19 Site: 1030 Prob: 1.000000
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