--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 25 20:35:49 WET 2016
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=CLUSTALW2
tcoffee.params=
tcoffee.maxSeqs=0
codeml.bin=codeml
mrbayes.tburnin=2500
codeml.dir=
input.sequences=
mrbayes.pburnin=2500
mrbayes.bin=mb_adops
tcoffee.bin=t_coffee_ADOPS
mrbayes.dir=/usr/bin/
tcoffee.dir=
tcoffee.minScore=3
input.fasta=/opt/ADOPS/1/5PtaseI-PB/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
(Use the harmonic mean for Bayes factor comparisons of models)
(Values are saved to the file /opt/ADOPS/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -4082.08 -4102.10
2 -4081.66 -4100.16
--------------------------------------
TOTAL -4081.85 -4101.55
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run2.p":
Summaries are based on a total of 3002 samples from 2 runs.
Each run produced 2001 samples of which 1501 samples were included.
Parameter summaries saved to file "/opt/ADOPS/1/5PtaseI-PB/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 0.792332 0.003858 0.674209 0.915036 0.791070 1360.41 1430.71 1.000
r(A<->C){all} 0.092136 0.000236 0.065148 0.124305 0.091030 994.10 1084.55 1.000
r(A<->G){all} 0.277879 0.000960 0.220915 0.339648 0.276815 775.02 1024.41 1.000
r(A<->T){all} 0.077631 0.000216 0.049040 0.106012 0.076891 831.03 998.86 1.000
r(C<->G){all} 0.103459 0.000282 0.072710 0.136586 0.102804 931.28 1041.02 1.000
r(C<->T){all} 0.395887 0.001073 0.329778 0.457849 0.395170 785.07 922.60 1.000
r(G<->T){all} 0.053009 0.000176 0.027774 0.079523 0.052377 1022.31 1153.44 1.000
pi(A){all} 0.280606 0.000141 0.256989 0.303160 0.280586 937.38 1063.64 1.000
pi(C){all} 0.241643 0.000127 0.220478 0.263679 0.241417 822.03 1057.65 1.000
pi(G){all} 0.229851 0.000131 0.208545 0.252974 0.229730 946.33 962.57 1.002
pi(T){all} 0.247900 0.000129 0.223819 0.268950 0.247951 1058.51 1169.56 1.000
alpha{1,2} 0.150232 0.000394 0.113824 0.189729 0.148777 1232.59 1325.92 1.000
alpha{3} 2.881911 0.663871 1.421088 4.459782 2.775990 1274.78 1350.86 1.000
pinvar{all} 0.378688 0.002217 0.290828 0.473814 0.381450 1321.93 1333.48 1.000
------------------------------------------------------------------------------------------------------
* Convergence diagnostic (ESS = Estimated Sample Size); min and avg values
correspond to minimal and average ESS among runs.
ESS value below 100 may indicate that the parameter is undersampled.
+ Convergence diagnostic (PSRF = Potential Scale Reduction Factor; Gelman
and Rubin, 1992) should approach 1.0 as runs converge.
Setting sumt conformat to Simple
--- CODEML SUMMARY
Model 1: NearlyNeutral -3580.847241
Model 2: PositiveSelection -3580.847254
Model 0: one-ratio -3621.141036
Model 3: discrete -3576.040902
Model 7: beta -3576.743784
Model 8: beta&w>1 -3576.512053
Model 0 vs 1 80.58759000000009
Model 2 vs 1 2.5999999706982635E-5
Model 8 vs 7 0.4634619999997085
>C1
MESAQEDASSTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIAVAQPRFL
ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVNEIIQSDDWTYGMIGEAVCMGDHKVLRIPQLYRSYRRAWRTW
>C2
MDSAQEDASSTDVFLVTANVGSLFEDPERLLQLWLNEFLAKIAVAQPRFL
ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENVKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVNEIIQSDDWTYGMIGEAVCMGDHKALRIPQLYRSYRRAWRTW
>C3
MDSAQEDASSTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIARAQPRFL
ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVNEIIQGDDWTYGMIGEAVCMGDHKALRIPQLSRSYRRAWRTW
>C4
MDSAQEDASCTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIAHAQPRFL
GLHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMADFTCVHIFMDEDFKSAE
HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVNEIIQSDDWTYGMIGEAVCMGDHKALRIPQLSRSYRRAWRTW
>C5
MDSAQEEDSCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKISHVQPRFL
ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
HFTALGSLYFVHKDVTSLKIWNFLTHSWEESLQDIQDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVHEIIRSDDWTYGMIGEAVCMGDHKAPRIPLVLPSCRRAWRTW
>C6
MDTAQEDGTCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKIAHVQPRFL
ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVHEIIRSDDWTYGMIGESVCMGDHKoooooooooooooooooo
>C7
MDSAQEDGTCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKISHVQPRFL
ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVQEIIRSDDWTYGMIGEAVCMGDHKoooooooooooooooooo
>C8
MDSAQEDGSCTDIFLVTANVGSLFEDPERLLQLWLNEFLAKISHVQPRFL
ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMADFTCVHIFMDEDFKSAE
HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVHEIIRGDDWTYGMIGEGVCMGDHKALQIPLVFPNYRRAWRTW
>C9
MDSAQEDGSGTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISQVAPKFL
ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPELADFTCVHIFMDEDFKSAE
HFTALGSLYFVHQDVASLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
ELTENLTAHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDVLVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVHEIIRSDDWKYGMIGEAVCMGDHKALRIPPAFRSYRKLWRTW
>C10
MDSAQEDGSSTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISIVQPKFL
ALHLQEVGGKTYEKSMEYVQEFIKCLCDSPELADFTCVHIFMDEDFKSAE
HFTALGSLYFVHQDVASLKIWNFLTHNWEESLQDTKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFVFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDILVEYPIMFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVQEIIRSDDWTYGMIGEAVCMGDHKALRIPPAFRSCRRAWRTW
>C11
MDSAQEDGVCTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISIVQPKFL
ALHLQEVGGKTYEKSMEYVQEFIKCLCDAPEMAQFTCVHIFMDEDFKSAE
HFTALGSLYFVHQDVASLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
KEKSKFPQHFFPECKWSRKGFMRTRWEVNGTVIDLVNIHLFHDASNLAAC
ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFVFGDFNFRCDTEGVVK
ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
DWLKKFDRELEPLKDILVEYPIKFVPSYPFEEDPEMPTDYMSTRCPAWCD
RILMSPQVHEIIRSDDWTYGMIGEAVCMGDHKALQIPPEYQSCRRAWQTW
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE: ], CPU=0.00 sec, SCORE=100, Nseq=11, Len=400
C1 MESAQEDASSTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIAVAQPRFL
C2 MDSAQEDASSTDVFLVTANVGSLFEDPERLLQLWLNEFLAKIAVAQPRFL
C3 MDSAQEDASSTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIARAQPRFL
C4 MDSAQEDASCTDVFLVTANVGSLFEDPERLLQLWLSEFLAKIAHAQPRFL
C5 MDSAQEEDSCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKISHVQPRFL
C6 MDTAQEDGTCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKIAHVQPRFL
C7 MDSAQEDGTCTDVFLVTANVGSLFEDPERLLQLWLHEFLAKISHVQPRFL
C8 MDSAQEDGSCTDIFLVTANVGSLFEDPERLLQLWLNEFLAKISHVQPRFL
C9 MDSAQEDGSGTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISQVAPKFL
C10 MDSAQEDGSSTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISIVQPKFL
C11 MDSAQEDGVCTDIFLVTANVGSLFEDPERLLQLWLHEFLAKISIVQPKFL
*::***: **:********************** ******: . *:**
C1 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
C2 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
C3 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
C4 GLHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMADFTCVHIFMDEDFKSAE
C5 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
C6 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
C7 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMGDFTCVHIFMDEDFKSAE
C8 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPEMADFTCVHIFMDEDFKSAE
C9 ALHLQEVGGKTYEKSMEYVQEFIRCLCDAPELADFTCVHIFMDEDFKSAE
C10 ALHLQEVGGKTYEKSMEYVQEFIKCLCDSPELADFTCVHIFMDEDFKSAE
C11 ALHLQEVGGKTYEKSMEYVQEFIKCLCDAPEMAQFTCVHIFMDEDFKSAE
.**********************:****:**:.:****************
C1 HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT
C2 HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT
C3 HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
C4 HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
C5 HFTALGSLYFVHKDVTSLKIWNFLTHSWEESLQDIQDKHIYSGNIETIAT
C6 HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT
C7 HFTALGSLYFVHKDVASLKIWNFLTHSWEESLQDVKDKHIYSGNIETIAT
C8 HFTALGSLYFVHKDVDSLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
C9 HFTALGSLYFVHQDVASLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
C10 HFTALGSLYFVHQDVASLKIWNFLTHNWEESLQDTKDKHIYSGNIETIAT
C11 HFTALGSLYFVHQDVASLKIWNFLTHSWEESLQDIKDKHIYSGNIETIAT
************:** **********.******* :**************
C1 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C2 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C3 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C4 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C5 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C6 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C7 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C8 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C9 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C10 KEKSKFPQHFFPECKWSRKGFMRTRWEINGTVIDLVNIHLFHDASNLAAC
C11 KEKSKFPQHFFPECKWSRKGFMRTRWEVNGTVIDLVNIHLFHDASNLAAC
***************************:**********************
C1 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C2 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C3 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C4 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C5 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C6 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C7 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C8 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C9 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFLFGDFNFRCDTEGVVK
C10 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFVFGDFNFRCDTEGVVK
C11 ENFPSVYCKTRRRALVHTIERFHLDEQNGTVPFFVFGDFNFRCDTEGVVK
**********************************:***************
C1 ELTENLTPHRVQNVKNENDKIHYRNSTGNNVLTVGKKEFSHADHQLKFKE
C2 ELTENLTPHRVQNVKNENVKIHYR 