--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Sat Nov 12 00:45:34 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-PD/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/2/Abl-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Abl-PD/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-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -14935.82 -14951.49
2 -14936.37 -14953.09
--------------------------------------
TOTAL -14936.06 -14952.58
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS/2/Abl-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/2/Abl-PD/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-PD/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 0.787466 0.001051 0.723095 0.849453 0.786687 1477.98 1482.74 1.000
r(A<->C){all} 0.081350 0.000066 0.065749 0.097226 0.081102 1085.96 1091.11 1.000
r(A<->G){all} 0.237455 0.000222 0.206450 0.264577 0.237114 919.23 952.55 1.000
r(A<->T){all} 0.164295 0.000241 0.133557 0.194215 0.163796 901.91 947.13 1.000
r(C<->G){all} 0.040937 0.000022 0.031787 0.050197 0.040800 986.75 1134.80 1.001
r(C<->T){all} 0.379734 0.000345 0.342372 0.414997 0.379931 748.04 778.55 1.000
r(G<->T){all} 0.096229 0.000106 0.076887 0.116455 0.095942 1124.49 1143.98 1.000
pi(A){all} 0.232558 0.000034 0.220998 0.243320 0.232601 969.00 1052.30 1.000
pi(C){all} 0.320617 0.000039 0.308509 0.332443 0.320471 996.34 1052.06 1.001
pi(G){all} 0.284757 0.000040 0.271639 0.296079 0.284628 967.66 1072.69 1.000
pi(T){all} 0.162068 0.000024 0.152608 0.171882 0.161850 929.90 996.92 1.000
alpha{1,2} 0.130354 0.000076 0.112894 0.147104 0.130179 1382.96 1414.86 1.000
alpha{3} 6.611760 1.625309 4.265224 9.180761 6.486721 1311.35 1406.18 1.000
pinvar{all} 0.378240 0.000455 0.339652 0.423048 0.377980 1209.64 1325.05 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 -13576.935707
Model 2: PositiveSelection -13576.935708
Model 0: one-ratio -13704.788551
Model 3: discrete -13568.334719
Model 7: beta -13568.905111
Model 8: beta&w>1 -13568.541213
Model 0 vs 1 255.7056879999982
Model 2 vs 1 2.0000006770715117E-6
Model 8 vs 7 0.7277959999992163
>C1
MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP
LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP
TVGLNIFTEHNGTKHSSFRGHPGKYHMNLEALLQSRPLPHIPAGSTAASL
LADAAELQQHQQDSGGLGLQGSSLGGGHSSTTSVFESAHRWTSKENLLAP
GPEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSGEWCEAHSDS
GNVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESE
SSPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVP
HEGHGLITPLLYPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQY
GEVYEAVWKRYGNTVAVKTLKEDTMALKDFLEEAAIMKEMKHPNLVQLIG
VCTREPPFYIITEFMSHGNLLDFLRSAGRETLDAVALLYMATQIASGMSY
LESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYTAHAGAKFPI
KWTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPAIDLTDVYHKLD
KGYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHMFQESSIT
EAVEKQLNANATSASSSAPSTSGVATGGGATTTTAASGCASSSSATASLS
LTPQMVKKGLPGGQALTPNAHHNDPHQQQASTPMSETGSTSTKLSTFSSQ
GKGNVQMRRTTNKQGKQAPAPPKRTSLLSSSRDSTYREEDPANARCNFID
DLSTNGIHKLKTANYFSQTLSRNFKTQIPTHHTHQIRTQQQQQQQSVQQQ
QQIVPLSVQQQAHQQQQKQQQYSIKKSSSCSSFLYDILFRGLARDINSLT
QRYDSETDPAADPDTDATGDSLEQSLSQVIAAPVTNKMQHSLHSGGGGGG
IGPRSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQLHSQAPGPGPPSTQP
HHGNNGVVTSAHPITVGALDVMNVKQVVNRYGTLPKGARIGAYLDSLEDS
SEAAPALPATAPSLPPANGHATPPAARLNPKASPIPPQQMIRSNSSGGVT
MQNNAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGVASGVQ
PALANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPN
NGNISNGNGTNNNDSSHNDVSNIAPSVEEASSRFGVSLRKREPSTDSCSS
LGSPPEDLKEKLITEIKAAGKDTAPASHLANGSGIAVVDPVSLLVTELAE
SMNLPKPPPQQQQKLTNGNSTGSGFKAQLKKVEPKKMSAPMPKAEPANTI
IDFKAHLRRVDKEKEPATPAPAPATVAVANNANCNTTGTLNRKEDGSKKF
SQAMQKTEIKIDVTNSNVEADAGAAGEGDLGKRRSTDDEEQSHTEGLGSG
GQGSADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAKLTEPASSASS
TQISRESILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNILHNSCVIFAE
NGAMPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERLVAEVGQSLRQ
ISNALNRooooooooooooooooooooooo
>C2
MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP
LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP
TVGLNIFTEHNGTKHSSFRGHPGKYHMNLEALLQSRPLPHIPAGSTAASL
LADAAELQQHQQDSGGLGLQGSSLGGGHSSTTSVFESAHRWTSKENLLAP
GPEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSGEWCEAHSDS
GNVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESE
SSPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVP
HEGHGLITPLLYPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQY
GEVYEAVWKRYGNTVAVKTLKEDTMALKDFLEEAAIMKEMKHPNLVQLIG
VCTREPPFYIITEFMSHGNLLDFLRSAGRETLDAVALLYMATQIASGMSY
LESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYTAHAGAKFPI
KWTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPGIDLTDVYHKLE
KGYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHMFQESSIT
EAVEKQLNANATSASSSAPSTSGVATGGGATTTTAASGCASSSSATASLS
LTPQMVKKGLSGGQSLTPNAHHNDPHQQQASTPMSETGSTSTKLSTFSSQ
GKGNVQMRRTTNKQGKQAPAPPKRTSLLSSSRDSTYREEDPANARCNFID
DLSTNGIHKLKTANYFSQTLSRNFKTQIPTQHTHQIRTQQQQQQQSVQQQ
QQTVPLSVQQQPHQQQKQQQYSIKKSSSCSSFLYDILFRGLARDINSLTQ
RYDSETDPAGDPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGGI
GPRSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPQAPGPGPPSTQPH
HGNNGVLTSAHPITVGALEVMNVKQVVNRYGTLPKGARIGAYLDSLEDST
EAAPPLPATAPSLPPANGHATPPSARLNPKASPIPPQQMIRSNSSGGVTM
QNNAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRSASGLASGVQP
ALANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNN
GNISNGNGSNNNDSSHNDVSNIAPSVEEASSRFGVSLRKREPSTDSCSSL
GSPPEDLKEKLITEIKAAGKESAPASHLANGSGIAVVDPVSLLVTELAES
MNLPKSPPQQQQKLTNGNGTGSGFKAQLKKVEPKKMSAPMPKAEPASTII
DFKAHLRRVDKEKEPAAPAPAPVAVANNANCNTTGTLNRKEDSSKKFSQA
MQKTEIKIDVTNSNVEADAGATGEGDLGKRRSTDDEEQSHTEGLGSGGQG
AADMTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAKLTEPASSASSTQI
SRESILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNILHNSCVIFAENGA
MPPHSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERLVAEVGQSLRQISN
ALNRoooooooooooooooooooooooooo
>C3
MGAQQGKDRGAHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVNSAP
LGGGSTLRGSRIKSSSSGVASGSGSGGGGGSGSGLSQRSGGHKDARCNPT
VGLNIFTEHNGTKHSSFRGHPGKYHMNLEALLQSRPLPHIPAGSTAASLL
ADAAELQQHQQDSGGLGLQGSSLGGGHSSTTSVFESAHRWTSKENLLAPG
PEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSGEWCEAHSDSG
NVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESES
SPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVPH
EGHGLITPLLYPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQYG
EVYEAVWKRYGNTVAVKTLKEDTMALKDFLEEAAIMKEMKHPNLVQLIGV
CTREPPFYIITEFMSHGNLLDFLRSAGRETLDAVALLYMATQIASGMSYL
ESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYTAHAGAKFPIK
WTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPGIDLTDVYHKLEK
GYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHMFQESSITE
AVEKQLNANATSASSSAPSTSGVATGGGATTTTAASGCASSSSATASLSL
TPQMVKKGLPGGQSLTPNAHHNDSHQQQASTPMSETGSTSTKLSTFSSQG
KGNVQMRRTTNKQGKQAPAPPKRTSLLSSSRDSTYREEDPATARCNFIDD
LSTNGIHKLKTANYFSQTLSRNFKTQIPTHHTHQIRTQLQQQQSVQQQTV
PLPVQQQQPQHQKQKQQQYSIKKSSSCSSFLYDILFRGLARDINSLTQRY
DSETDPAADPDTDATGDSLEQSLSQVIAAPATNKMQHSLHSGGGGGGIGP
RSSQQHSSFKRPTGTPVMGNRGLETRQSKRSQHHPLAPGPGPPATQPHHG
NNGVVASAHPITVGALEVMNVKQVVNRYGTLPKVARIGAYLDSLEDSTEA
APALPATAPALPPANGHATPPAARINPKASPIPPQQMIRSNSSGGVTMQN
NAAASLNKLQRHRTTTEGTMMTFSSFRAGGSSSSPKRNATGAASGVQPAL
ANLEFPPPPLDLPPPPEEFEGGPPPPPPAPESAVQAIQQHLHAQLPNNGN
ISNGNGTNNNDSSHNDVSNTAPSVEEASSRFGVSLRKREPSTDSCSSLGS
PPEDLKEKLITEIKAAGKDSAPASQLANGSGIAVVDPVSLLVTELAESMN
LPKPPPQQQKLTNGNGTGSGFKAQLKKVEPKKMSAPIAKAEPANTIIDFK
AHLRRVDKEKEPAAPAPAPVAVTNNANCNTTGTLNRKEDSSKKFSQAMQK
TEIKIDVTNSNVEADAGAAGEGDLGKRRSTDDEEQSHSDGLGSGGQGAAD
MTQSLYEQKPQIQQKPAVPHKPTKLTIYATPIAKLAEPASSASSTQISRD
SILELVGLLEGSLKHPVNAIAGSQWLQLSDKLNILHNSCVIFAENGAMPP
HSKFQFRELVTRVEAQSQHLRSAGSKNVQDNERLVAEVGQSLRQISNALN
Rooooooooooooooooooooooooooooo
>C4
MGAQQGKDRGGHSGGGGSGAPVSCIGLSSSPVASVSPHCISSSSGVSSAP
LGGGSTLRGSRIKSSSSGVASGSGSGGGGGGSGSGLSQRSGGHKDARCNP
TVGLNIFTEHNGTKHSSFRGHPGKYHMNLEALLQSRPLPHIPAGSTAASL
LADAAELQQHQQDSSGLGLQGSSLGGGHSSTTSVFESAHRWTSKENLLAP
GPEEDDPQLFVALYDFQAGGENQLSLKKGEQVRILSYNKSGEWCEAHSDS
GNVGWVPSNYVTPLNSLEKHSWYHGPISRNAAEYLLSSGINGSFLVRESE
SSPGQRSISLRYEGRVYHYRISEDPDGKVFVTQEAKFNTLAELVHHHSVP
HEGHGLITPLLYPAPKQNKPTVFPLSPEPDEWEICRTDIMMKHKLGGGQY
GEVYEAVWKRYGNTVAVKTLKEDTMALKDFLEEAAIMKEMKHPNLVQLIG
VCTREPPFYIITEFMSHGNLLDFLRSAGRETLDAVALLYMATQIASGMSY
LESRNYIHRDLAARNCLVGDNKLVKVADFGLARLMRDDTYTAHAGAKFPI
KWTAPEGLAYNKFSTKSDVWAFGVLLWEIATYGMSPYPGIDLTDVYHKLE
KGYRMERPPGCPPEVYDLMRQCWQWDATDRPTFKSIHHALEHM
