--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Sun Dec 04 13:27:01 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/357/Prp18-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/357/Prp18-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/357/Prp18-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/357/Prp18-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3863.18         -3877.11
2      -3862.76         -3878.19
--------------------------------------
TOTAL    -3862.95         -3877.79
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/357/Prp18-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/357/Prp18-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/357/Prp18-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}         1.988651    0.024654    1.680483    2.290648    1.986669    906.75    998.46    1.000
r(A<->C){all}   0.054360    0.000131    0.032271    0.076571    0.053681    703.20    850.35    1.000
r(A<->G){all}   0.225000    0.000753    0.173118    0.278396    0.223918    769.21    887.86    1.000
r(A<->T){all}   0.086574    0.000509    0.044045    0.130266    0.084776    706.04    781.74    1.000
r(C<->G){all}   0.024184    0.000041    0.012336    0.037039    0.023764    908.27   1073.29    1.000
r(C<->T){all}   0.550399    0.001359    0.480448    0.619685    0.550544    629.45    761.33    1.000
r(G<->T){all}   0.059484    0.000213    0.030610    0.086484    0.058617    824.48    979.61    1.000
pi(A){all}      0.279323    0.000176    0.254477    0.306338    0.278788   1060.99   1204.48    1.000
pi(C){all}      0.295763    0.000163    0.271770    0.322374    0.295434   1129.55   1253.16    1.000
pi(G){all}      0.276023    0.000165    0.250510    0.300198    0.276021   1180.57   1223.21    1.000
pi(T){all}      0.148891    0.000095    0.130216    0.168270    0.148623    925.26    973.08    1.000
alpha{1,2}      0.087789    0.000056    0.074184    0.103068    0.087496   1264.73   1311.72    1.000
alpha{3}        4.055741    0.943876    2.324073    5.975230    3.942780   1236.95   1274.23    1.000
pinvar{all}     0.202799    0.001364    0.129628    0.274844    0.202854   1500.71   1500.85    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	-3497.801723
Model 2: PositiveSelection	-3497.801723
Model 0: one-ratio	-3498.544633
Model 3: discrete	-3483.880694
Model 7: beta	-3483.949264
Model 8: beta&w>1	-3483.952656


Model 0 vs 1	1.485819999999876

Model 2 vs 1	0.0

Model 8 vs 7	0.006784000000152446
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MDILKAEIARKRKLLEQRQLVDEKKKYFRRGDLNAKNTEEVLQKVGYIKQ
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MDILKAEIARKRKLLEQKQLVDEKKKYFRRGDLNAKNTEEVLQKVGYIKQ
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LLNRNYITASDAYLEMAIGNAPWPIGVTMVGIHARTGREKIFSKNVAHVM
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LLNRNYITASDAYLEMAIGNAPWPIGVTMVGIHARTGREKIFSKNVAHVM
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>C10
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CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=100, Nseq=11, Len=340 

C1              MDILKAEIARKRKLLEQRQLVDEKKKYFRRGDLNAKNTEEVLQKVGYIKQ
C2              MDILKAEIARKRKLLEQKQLVDEKKKYFRRGDLNAKNTEEVLQKVGYIKQ
C3              MDILKAEIARKRKLLEQKQLVDEKKKYFRRGDLNAKNTEEVLQKVGYIKQ
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C8              MDILKAEIARKRKLLEQKQLVDEKKKYFRRGDLNAKDTEEVLQKVGYKKQ
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C11             MDILKAEIARKRKLLEQKQLVDDKKKYFRRGDLNAKDTEEVLQKVGYKKQ
                *****************:****::************ ********** **

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C4              ESVEAQGQTTEGAYSFVADGQNILPRTEVIRRLRERGEPILIFGETEPEA
C5              ESVEAQGQTSEGAYSFVADGQNILPRTEVIRRLRERGEPIFIFGETEPEA
C6              ESVEAQGQTTEGAYSFVADGQNILPRAEVIRRLRERGEPILIFGETEPEA
C7              ESVEAQGQSTEGAYSFVADGQNILPRTEVIRRLRERGEPILIFGETEPEA
C8              ESVEAQGQTTEGAYSFVADGQNILPRAEVIRRLRERGEPILIFGETEPEA
C9              ESVEAQGQITEGAYSFVADGQNILPRTEVIRRLRERGEPILIFGETEPEA
C10             ESVEAQGQTTEGAYSFVADGQNILPRTEVIRRLRERGEPILIFGETEPEA
C11             ESVEAQGQTTEGAYSFVADGQNILPRAEVIRRLRERGEPILIFGETEPEA
                ******** :****************:*************:*********

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C2              FDRLRQCEISQPEANRGFRNDFQEAMEQVDAAYLQEMFANTPTTKEDKKS
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                ****************************************:*..******

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                *:*****:******* ** :******:***********************

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C3              SKHEKMSTKVKMTRVIYTQTKEYVKPLFRKLKHHTLPEDILDSLRDICKH
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                **************************************************

C1              LLNRNYITASDAYLEMAIGNAPWPIGVTMVGIHARTGREKIFSKNVAHVM
C2              LLNRNYITASDAYLEMAIGNAPWPIGVTMVGIHARTGREKIFSKNVAHVM
C3              LLNRNYITASDAYLEMAIGNAPWPIGVTMVGIHARTGREKIFSKNVAHVM
C4              LLNRNYITASDAYLEMAIGNAPWPIGVTMVGIHARTGREKIFSKNVAHVM
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C10             LLNRNYITASDAYLEMAIGNAPWPIGVTMVGIHARTGREKIFSKNVAHVM
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                **************************************************

C1              NDETQRKYIQGLKRLMTKCQEYFPTDPSKCVEYVSKKDRE
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C4              NDETQRKYIQGLKRLMTKCQEYFPTDPSKCVEYVSKKDRE
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                ****************************************




PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427)
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-prot_min_cov  	D	[40] 	40 
-pdb_type      	S	[0] 	d
-pdb_min_sim   	D	[35] 	35 
-pdb_max_sim   	D	[100] 	100 
-pdb_min_cov   	D	[50] 	50 
-pdb_blast_server	W_F	[0] 	EBI
-blast         	W_F	[0] 
-blast_server  	W_F	[0] 	EBI
-pdb_db        	W_F	[0] 	pdb
-protein_db    	W_F	[0] 	uniprot
-method_log    	W_F	[0] 	no
-struc_to_use  	S	[0] 
-cache         	W_F	[0] 	use
-align_pdb_param_file	W_F	[0] 	no
-align_pdb_hasch_mode	W_F	[0] 	hasch_ca_trace_bubble
-external_aligner	S	[0] 	NO
-msa_mode      	S	[0] 	tree
-master        	S	[0] 	no
-blast_nseq    	D	[0] 	0 
-lalign_n_top  	D	[0] 	10 
-iterate       	D	[1] 	0 
-trim          	D	[0] 	0 
-split         	D	[0] 	0 
-trimfile      	S	[0] 	default
-split         	D	[0] 	0 
-split_nseq_thres	D	[0] 	0 
-split_score_thres	D	[0] 	0 
-check_pdb_status	D	[0] 	0 
-clean_seq_name	D	[0] 	0 
-seq_to_keep   	S	[0] 
-dpa_master_aln	S	[0] 
-dpa_maxnseq   	D	[0] 	0 
-dpa_min_score1	D	[0] 
-dpa_min_score2	D	[0] 
-dpa_keep_tmpfile	FL	[0] 	0
-dpa_debug     	D	[0] 	0 
-multi_core    	S	[0] 	templates_jobs_relax_msa_evaluate
-n_core        	D	[0] 	0 
-max_n_proc    	D	[0] 	0 
-lib_list      	S	[0] 
-prune_lib_mode	S	[0] 	5
-tip           	S	[0] 	none
-rna_lib       	S	[0] 
-no_warning    	D	[0] 	0 
-run_local_script	D	[0] 	0 
-plugins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  340 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:
ugins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C10 Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C11 Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C2  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C3  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C4  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C5  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C6  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C7  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C8  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C9  Length  340 type PROTEIN Struct Unchecked

	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln S/opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.alnugins       	S	[0] 	default
-proxy         	S	[0] 	unset
-email         	S	[0] 
-clean_overaln 	D	[0] 	0 
-overaln_param 	S	[0] 
-overaln_mode  	S	[0] 
-overaln_model 	S	[0] 
-overaln_threshold	D	[0] 	0 
-overaln_target	D	[0] 	0 
-overaln_P1    	D	[0] 	0 
-overaln_P2    	D	[0] 	0 
-overaln_P3    	D	[0] 	0 
-overaln_P4    	D	[0] 	0 
-exon_boundaries	S	[0] 
-dump          	S	[0] 	no
-display       	D	[0] 	100 

INPUT FILES
	Input File (S) /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 11 SEQUENCES  [PROTEIN]
  Input File /opt/ADOPS/357/Prp18-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln Seq C1  Length  340 type PROTEIN Struct Unchecked
  Input File /opt/ADOPS/35