--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Nov 11 22:55:39 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/2/Abl-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Abl-PA/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/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -15110.38 -15129.90
2 -15110.60 -15126.07
--------------------------------------
TOTAL -15110.48 -15129.23
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Abl-PA/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/2/Abl-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 0.824864 0.001191 0.764090 0.900067 0.823901 1355.93 1428.47 1.000
r(A<->C){all} 0.080029 0.000063 0.065827 0.096519 0.079969 855.08 968.46 1.000
r(A<->G){all} 0.242900 0.000235 0.213529 0.273674 0.242324 817.99 889.51 1.000
r(A<->T){all} 0.164673 0.000243 0.134402 0.194552 0.164115 1000.79 1006.32 1.003
r(C<->G){all} 0.035059 0.000018 0.026764 0.043025 0.034931 1319.24 1323.85 1.000
r(C<->T){all} 0.381759 0.000340 0.344894 0.416450 0.381958 731.41 738.28 1.000
r(G<->T){all} 0.095579 0.000099 0.076502 0.115008 0.095383 842.60 954.21 1.002
pi(A){all} 0.224361 0.000032 0.213681 0.235634 0.224226 1017.12 1027.58 1.000
pi(C){all} 0.324495 0.000039 0.312512 0.337098 0.324372 897.39 917.82 1.000
pi(G){all} 0.291512 0.000039 0.279433 0.303503 0.291614 864.00 1010.08 1.000
pi(T){all} 0.159631 0.000022 0.150534 0.168617 0.159663 926.87 1017.94 1.001
alpha{1,2} 0.127424 0.000063 0.111068 0.141948 0.127338 1361.57 1400.88 1.000
alpha{3} 6.619604 1.566201 4.343072 9.157669 6.493033 1462.92 1481.96 1.000
pinvar{all} 0.376988 0.000417 0.336003 0.416148 0.377277 1183.71 1185.43 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 -13690.531085
Model 2: PositiveSelection -13690.531085
Model 0: one-ratio -13807.238424
Model 3: discrete -13682.842607
Model 7: beta -13685.517501
Model 8: beta&w>1 -13683.005896
Model 0 vs 1 233.41467799999737
Model 2 vs 1 0.0
Model 8 vs 7 5.023209999999381
>C1
MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP
LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP
TVGLNIFTEHNEALLQSRPLPHIPAGSTAASLLADAAELQQHQQDSGGLG
LQGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQA
GGENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLE
KHSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYH
YRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQN
KPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVK
TLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHG
NLLDFLRSAGRETLDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLV
GDNKLVKVADFGLARLMRDDTYTAHAGAKFPIKWTAPEGLAYNKFSTKSD
VWAFGVLLWEIATYGMSPYPAIDLTDVYHKLDKGYRMERPPGCPPEVYDL
MRQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANATSASSSA
PSTSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLPGGQALTP
NAHHNDPHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQA
PAPPKRTSLLSSSRDSTYREEDPANARCNFIDDLSTNGLARDINSLTQRY
DSETDPAADPDTDATGDSLEQSLSQVIAAPVTNKMQHSLHSGGGGGGIGP
RSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQLHSQAPGPGPPSTQPHHG
NNGVVTSAHPITVGALDVMNVKQVVNRYGTLPKGARIGAYLDSLEDSSEA
APALPATAPSLPPANGHATPPAARLNPKASPIPPQQMIRSNSSGGVTMQN
NAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGVASGVQPAL
ANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGN
ISNGNGTNNNDSSHNDVSNIAPSVEEASSRFGVSLRKREPSTDSCSSLGS
PPEDLKEKLITEIKAAGKDTAPASHLANGSGIAVVDPVSLLVTELAESMN
LPKPPPQQQQKLTNGNSTGSGFKAQLKKVEPKKMSAPMPKAEPANTIIDF
KAHLRRVDKEKEPATPAPAPATVAVANNANCNTTGTLNRKEDGSKKFSQA
MQKTEIKIDVTNSNVEADAGAAGEGDLGKRRSTGSINSLKKLWEQQPPAP
DYATSTILQQQPSVVNGGGTPNAQLSPKYGMKSGAINTVGTLPAKLGNKQ
PPAAPPPPPPNCTTSNSSTTSISTSSRDCTSRQQASSTIKTSHSTQLFTD
DEEQSHTEGLGSGGQGSADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATP
IAKLTEPASSASSTQISRESILELVGLLEGSLKHPVNAIAGSQWLQLSDK
LNILHNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDN
ERLVAEVGQSLRQISNALNRooooooooooooooooo
>C2
MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP
LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP
TVGLNIFTEHNEALLQSRPLPHIPAGSTAASLLADAAELQQHQQDSGGLG
LQGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQA
GGENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLE
KHSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYH
YRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQN
KPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVK
TLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHG
NLLDFLRSAGRETLDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLV
GDNKLVKVADFGLARLMRDDTYTAHAGAKFPIKWTAPEGLAYNKFSTKSD
VWAFGVLLWEIATYGMSPYPGIDLTDVYHKLEKGYRMERPPGCPPEVYDL
MRQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANATSASSSA
PSTSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLSGGQSLTP
NAHHNDPHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQA
PAPPKRTSLLSSSRDSTYREEDPANARCNFIDDLSTNGLARDINSLTQRY
DSETDPAGDPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGGIGP
RSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPQAPGPGPPSTQPHHG
NNGVLTSAHPITVGALEVMNVKQVVNRYGTLPKGARIGAYLDSLEDSTEA
APPLPATAPSLPPANGHATPPSARLNPKASPIPPQQMIRSNSSGGVTMQN
NAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGLASGVQPAL
ANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGN
ISNGNGSNNNDSSHNDVSNIAPSVEEASSRFGVSLRKREPSTDSCSSLGS
PPEDLKEKLITEIKAAGKESAPASHLANGSGIAVVDPVSLLVTELAESMN
LPKSPPQQQQKLTNGNGTGSGFKAQLKKVEPKKMSAPMPKAEPASTIIDF
KAHLRRVDKEKEPAAPAPAPVAVANNANCNTTGTLNRKEDSSKKFSQAMQ
KTEIKIDVTNSNVEADAGATGEGDLGKRRSTGSINSLKKLWEQQPPASDY
ATSTILQQQPVVNGGGTQTAQLSPKYGMKSGAINTAGTLPAKLGNKPPPA
APPPPPPNCTTSNSSTTSISTSSRDCTSRQQASSTIKTSHSTQLFADDEE
QSHTEGLGSGGQGAADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAK
LTEPASSASSTQISRESILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNI
LHNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERL
VAEVGQSLRQISNALNRoooooooooooooooooooo
>C3
MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVNSAP
LGGGSTLRGSRIKSSSSGVASGSGSGGGGGSGSGLSQRSGGHKDARCNPT
VGLNIFTEHNEALLQSRPLPHIPAGSTAASLLADAAELQQHQQDSGGLGL
QGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQAG
GENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLEK
HSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHY
RISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQNK
PTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVKT
LKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHGN
LLDFLRSAGRETLDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLVG
DNKLVKVADFGLARLMRDDTYTAHAGAKFPIKWTAPEGLAYNKFSTKSDV
WAFGVLLWEIATYGMSPYPGIDLTDVYHKLEKGYRMERPPGCPPEVYDLM
RQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANATSASSSAP
STSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLPGGQSLTPN
AHHNDSHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQAP
APPKRTSLLSSSRDSTYREEDPATARCNFIDDLSTNGLARDINSLTQRYD
SETDPAADPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGGIGPR
SSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPLAPGPGPPATQPHHGN
NGVVASAHPITVGALEVMNVKQVVNRYGTLPKVARIGAYLDSLEDSTEAA
PALPATAPALPPANGHATPPAARINPKASPIPPQQMIRSNSSGGVTMQNN
AAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRNATGAASGVQPALA
NLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGNI
SNGNGTNNNDSSHNDVSNTAPSVEEASSRFGVSLRKREPSTDSCSSLGSP
PEDLKEKLITEIKAAGKDSAPASQLANGSGIAVVDPVSLLVTELAESMNL
PKPPPQQQKLTNGNGTGSGFKAQLKKVEPKKMSAPIAKAEPANTIIDFKA
HLRRVDKEKEPAAPAPAPVAVTNNANCNTTGTLNRKEDSSKKFSQAMQKT
EIKIDVTNSNVEADAGAAGEGDLGKRRSTGSINSLKKLWEQQPPAPDYAT
STILQQQPSVVNGGGTPNAQLSPKYGMKSGAPNTGGTLPAKLGNKPPPAA
PPPPPPNCTTSNLSTTSISTSSRDCTSRQQASSTIKTSHSTQLFTDDEEQ
SHSDGLGSGGQGAADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAKL
AEPASSASSTQISRDSILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNIL
HNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERLV
AEVGQSLRQISNALNRooooooooooooooooooooo
>C4
MGAQQGKDRGGHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP
LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP
TVGLNIFTEHNEALLQSRPLPHIPAGSTAASLLADAAELQQHQQDSSGLG
LQGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQA
GGENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLE
KHSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYH
YRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQN
KPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVK
TLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHG
NLLDFLRSAGRETLDAVALLYMATQIASGMSYLESRNYIHRDLAARNCLV
GDNKLVKVADFGLARLMRDDTYTAHAGAKFPIKWTAPEGLAYNKFSTKSD
VWAFGVLLWEIATYGMSPYPGIDLTDVYHKLEKGYRMERPPGCPPEVYDL
MRQCWQWDATDRPTFKSIHHALEHMFQESSITEAVEKQLNANATSASSSA
PSTSGVATGGGATTTTAASGCASSSSATASLSLTPQMVKKGLPGGQSLTP
NAHHTDPHQQQASTPMSETGSTSTKLSTFSSQGKGNVQMRRTTNKQGKQA
PAPPKRTSLLSSSRDSTYREEDPATARCNFIDDLSTNGFARDINSLTQRY
DSETDPAADPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGIGPR
SSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPLAPGPGPPATQPHHGN
NGVVTSAHPITVGALEVMNVKQVVNRYGTLPKGARIGAYLDSLEDSSEAA
PALPATAPSLPPANGHATPPAARINPKASPIPPQQMIRSNSSGGVTMQNN
AAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSATGVASGVQPALA
NLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGNI
SNGNGTNNNDSSHNDVSNTAPSVEEASSRFGVSLRKREPSTDSCSSLGSP
PEDLKEKLITEIKASGKDSAPTSHLANGSGIAVVDPVSQLFTELEESMKL
PKPPPQQQKLTNGNGTGSGFKAQLKKVEPKKMCAPMAKAEPANTIIDFKA
HLRRVDKEKEPAAPAPAPVPAAAPVAVTNNANCNTTGTLNRKEDSSKKFS
QVMQKTEIKIDVTNSNVEADAGAAGEGDLGKRRSTGSINSLKKLWEQQPP
APDYATSTILQQQPSVVNGGGTPNAQLSPKYGMKSGATNAGGTLPAKLGN
KPPPAAPPPPPPNCTTSNLSTTSISTSSRDFTSRQQASSTIKTSHSTQLF
TDDEEQSHSDGLGSGGQGAADMTQSLYEQKPQIQQKPVVPHKPTKLTIYA
TPIAKLAEPASSTQISRESILELVGLLEGSLKHPVNAIAGSQWLQLSDKL
NILHNSCVIFAENGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNE
RLVAEVGQSLRQISNALNRoooooooooooooooooo
>C5
MGAQQGKDRGAHSGGGGSAAPVSCIGLSSSPVASVSPHCISSSSGVSSAP
LGGGSTLRGSRIKSSSSGVVSGGGSGGGGGGSGSGLSQRSGGHKDPRCNP
SVGLNIFTEHNEALLQSRPLPHIPAGSAAASLLADAAEMQQHQQDSGGLG
LQGSSLGGGHSSTTSVFESAHRWTSKENLLAPGPEEDDPQLFVALYDFQA
GGENQLSLKKGEQVRILSYNKSGEWCEAHSDSGNVGWVPSNYVTPLNSLE
KHSWYHGPISRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYH
YRISEDPDGKVFVTQEAKFNTLAELVHHHSVPHEGHGLITPLLYPAPKQN
KPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYGEVYEAVWKRYGNTVAVK
TLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGVCTREPPFYIITEFMSHG
NLLD
