--- 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