--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Dec 09 16:31:58 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/443/Zip48C-PA/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS/443/Zip48C-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/443/Zip48C-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/443/Zip48C-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -3732.32         -3750.11
2      -3732.52         -3747.53
--------------------------------------
TOTAL    -3732.42         -3749.49
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS/443/Zip48C-PA/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS/443/Zip48C-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/443/Zip48C-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}         1.517565    0.014614    1.291632    1.755313    1.511958   1365.61   1433.30    1.000
r(A<->C){all}   0.150525    0.000531    0.106136    0.194644    0.149807    951.64    953.32    1.000
r(A<->G){all}   0.222011    0.000820    0.164962    0.276809    0.220507    893.03    938.24    1.000
r(A<->T){all}   0.115174    0.000838    0.062725    0.175343    0.113155    806.19    818.28    1.000
r(C<->G){all}   0.063261    0.000130    0.043481    0.086779    0.062716    856.34    943.23    1.000
r(C<->T){all}   0.411351    0.001222    0.343526    0.481963    0.410858    831.73    839.74    1.000
r(G<->T){all}   0.037677    0.000137    0.016522    0.061038    0.036742   1166.45   1236.92    1.002
pi(A){all}      0.181546    0.000121    0.158897    0.202949    0.181424   1129.69   1130.74    1.001
pi(C){all}      0.306172    0.000175    0.280468    0.331761    0.306081   1154.12   1174.57    1.000
pi(G){all}      0.302426    0.000179    0.276396    0.328630    0.302352   1014.99   1064.32    1.001
pi(T){all}      0.209855    0.000133    0.187805    0.232249    0.209839   1021.16   1052.11    1.000
alpha{1,2}      0.099787    0.000079    0.081400    0.115676    0.099211   1412.73   1456.86    1.000
alpha{3}        3.442387    0.707423    1.905176    5.127729    3.344959   1501.00   1501.00    1.000
pinvar{all}     0.332054    0.001433    0.258481    0.405543    0.332529   1198.15   1216.87    1.001
------------------------------------------------------------------------------------------------------
* 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	-3270.872409
Model 2: PositiveSelection	-3270.872409
Model 0: one-ratio	-3286.153778
Model 3: discrete	-3268.229859
Model 7: beta	-3270.640774
Model 8: beta&w>1	-3270.146761


Model 0 vs 1	30.562737999999626

Model 2 vs 1	0.0

Model 8 vs 7	0.9880259999999907
>C1
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKAKADIAIEDSKRNGVAPDRLASKSLDSFSDCLS
VQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEDALSQWKRIMLLVVAI
TVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAVSLP
LHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAGA
MIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo
>C2
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKAKADIAIEDSKRNGLASDRLASKSLDSFSDCLS
VQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLVVAI
TVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAVSLP
LHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAGA
MIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo
>C3
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKAKADIAIEDSKRNGLASDRLASKSLDSFSDCLS
VQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLVVAI
TVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAVSLP
LHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAGA
MIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo
>C4
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKDKADIAIEDSKRNGVASDRLASKSLDSFSDCLS
VQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLVVAI
TVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAVSLP
LHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAGA
MIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo
>C5
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFLPVSGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKDKADIAIEDSKRNGVPSDRLASKSLDSFSDCLS
VQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLVVAI
TVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAVSLP
LHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAGA
MIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo
>C6
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAETSHLYGVYAFLPVSGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKDKADIAIEDSKRNGGGASDRLASKSLDSFSDCL
SVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLVVA
ITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAVSL
PLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAG
AMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSo
>C7
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFLPVSGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKDKADIAIEDSKRNGGGASDRLASKSLDSFSDCL
SVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLVVA
ITVHNIPEGLAVGVSFGAIGTTNSSTFESARNLAIGIGIQNFPEGLAVSL
PLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAG
AMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSo
>C8
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFLPVSGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSNKDKADIAIEDSKRNGASDRLASKSLDSFSDCLS
VQHSGESRRRKKGSSINDMEQCTYTTPEEQQRAEEALSQWKRIMLLVVAI
TVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAVSLP
LHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAGA
MIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo
>C9
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFVPVAGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKDKADIAIEDSKRNGGASDRLASKSLDSFSDCLS
VQHSGESRRRKKGGSINEMEQCTYTTPEEQQRAEEALSQWKRIMLLVVAI
TVHNIPEGLAVGVSFGAIGTTNSSTFESARNLAIGIGIQNFPEGLAVSLP
LHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAGA
MIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo
>C10
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFVPVAGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKDKADIAIEDSKRNGGANAADRLASKSLDSFSDC
LSVQHSGESRRRKKGGSINEMEQCTYTTPEEQQRADEALSQWKRIMLLVV
AITVHNIPEGLAVGVSFGAIGTTNSSTFESARNLAIGIGIQNFPEGLAVS
LPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAA
GAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALS
>C11
MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
YLGLNSTNMMIQMTQSKDKADIAIEDAKRKSKSLDSFSDCLSVQHSGESR
RRKKQGSINEMEQCTYTTPEEQQRAEEALSQWKRIMLLVVAITVHNIPEG
LAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAVSLPLHAAGFSV
KRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFAAGAMIYIVSDD
ILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoooooooooo
CLUSTAL FORMAT for T-COFFEE Version_10.00.r1613 [http://www.tcoffee.org] [MODE:  ], CPU=0.00 sec, SCORE=99, Nseq=11, Len=354 

C1              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C2              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C3              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C4              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C5              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C6              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C7              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C8              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C9              MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C10             MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
C11             MIPGYGPVTQALLGTLLTWGLTAAGAALVIFVRGNQRRSLDAALGFAAGV
                **************************************************

C1              MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
C2              MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
C3              MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
C4              MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
C5              MIAASFWSLLKPAIEMAESSHLYGVYAFLPVSGGFLLGSIFVYGCDKLMS
C6              MIAASFWSLLKPAIEMAETSHLYGVYAFLPVSGGFLLGSIFVYGCDKLMS
C7              MIAASFWSLLKPAIEMAESSHLYGVYAFLPVSGGFLLGSIFVYGCDKLMS
C8              MIAASFWSLLKPAIEMAESSHLYGVYAFLPVSGGFLLGSIFVYGCDKLMS
C9              MIAASFWSLLKPAIEMAESSHLYGVYAFVPVAGGFLLGSIFVYGCDKLMS
C10             MIAASFWSLLKPAIEMAESSHLYGVYAFVPVAGGFLLGSIFVYGCDKLMS
C11             MIAASFWSLLKPAIEMAESSHLYGVYAFLPVAGGFLLGSIFVYGCDKLMS
                ******************:*********:**:******************

C1              YLGLNSTNMMIQMTQS-KAKADIAIEDSKRNG--VAPDRLASKSLDSFSD
C2              YLGLNSTNMMIQMTQS-KAKADIAIEDSKRNG--LASDRLASKSLDSFSD
C3              YLGLNSTNMMIQMTQS-KAKADIAIEDSKRNG--LASDRLASKSLDSFSD
C4              YLGLNSTNMMIQMTQS-KDKADIAIEDSKRNG--VASDRLASKSLDSFSD
C5              YLGLNSTNMMIQMTQS-KDKADIAIEDSKRNG--VPSDRLASKSLDSFSD
C6              YLGLNSTNMMIQMTQS-KDKADIAIEDSKRNGG-GASDRLASKSLDSFSD
C7              YLGLNSTNMMIQMTQS-KDKADIAIEDSKRNGG-GASDRLASKSLDSFSD
C8              YLGLNSTNMMIQMTQSNKDKADIAIEDSKRNG---ASDRLASKSLDSFSD
C9              YLGLNSTNMMIQMTQS-KDKADIAIEDSKRNGG-A-SDRLASKSLDSFSD
C10             YLGLNSTNMMIQMTQS-KDKADIAIEDSKRNGGANAADRLASKSLDSFSD
C11             YLGLNSTNMMIQMTQS-KDKADIAIEDAKRKS----------KSLDSFSD
                **************** * ********:**:.          ********

C1              CLSVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEDALSQWKRIMLLV
C2              CLSVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLV
C3              CLSVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLV
C4              CLSVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLV
C5              CLSVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLV
C6              CLSVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLV
C7              CLSVQHSGESRRRKKGASINEMEQCTYTTPEEQQRAEEALSQWKRIMLLV
C8              CLSVQHSGESRRRKKGSSINDMEQCTYTTPEEQQRAEEALSQWKRIMLLV
C9              CLSVQHSGESRRRKKGGSINEMEQCTYTTPEEQQRAEEALSQWKRIMLLV
C10             CLSVQHSGESRRRKKGGSINEMEQCTYTTPEEQQRADEALSQWKRIMLLV
C11             CLSVQHSGESRRRKKQGSINEMEQCTYTTPEEQQRAEEALSQWKRIMLLV
                *************** .***:***************::************

C1              VAITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAV
C2              VAITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAV
C3              VAITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAV
C4              VAITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAV
C5              VAITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAV
C6              VAITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAV
C7              VAITVHNIPEGLAVGVSFGAIGTTNSSTFESARNLAIGIGIQNFPEGLAV
C8              VAITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAV
C9              VAITVHNIPEGLAVGVSFGAIGTTNSSTFESARNLAIGIGIQNFPEGLAV
C10             VAITVHNIPEGLAVGVSFGAIGTTNSSTFESARNLAIGIGIQNFPEGLAV
C11             VAITVHNIPEGLAVGVSFGAIGSTNSSTFESARNLAIGIGIQNFPEGLAV
                **********************:***************************

C1              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C2              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C3              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C4              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C5              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C6              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C7              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C8              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C9              SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C10             SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
C11             SLPLHAAGFSVKRALWYGQLSGMVEPIFGVLGAVAVTFANLILPYALSFA
                **************************************************

C1              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo----
C2              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo----
C3              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo----
C4              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo----
C5              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo----
C6              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSo-----
C7              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSo-----
C8              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo----
C9              AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoo----
C10             AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALS------
C11             AGAMIYIVSDDILPEAHASGNGTIATWGTVSGFLIMMCLEVALSoooooo
                ********************************************      

C1              ----
C2              ----
C3              ----
C4              ----
C5              ----
C6              ----
C7              ----
C8              ----
C9              ----
C10             ----
C11             oooo
                    




PROGRAM: T-COFFEE Version_10.00.r1613 (2013-10-22 15:49:04 - Revision 1613 - Build 427)
-full_log      	S	[0] 
-genepred_score	S	[0] 	nsd
-run_name      	S	[0] 
-mem_mode      	S	[0] 	mem
-extend        	D	[1] 	1 
-extend_mode   	S	[0] 	very_fast_triplet
-max_n_pair    	D	[0] 	10 
-seq_name_for_quadruplet	S	[0] 	all
-compact       	S	[0] 	default
-clean         	S	[0] 	no
-do_self       	FL	[0] 	0
-do_normalise  	D	[0] 	1000 
-template_file 	S	[0] 
-setenv        	S	[0] 	0
-template_mode 	S	[0] 
-flip          	D	[0] 	0 
-remove_template_file	D	[0] 	0 
-profile_template_file	S	[0] 
-in            	S	[0] 
-seq           	S	[0] 
-aln           	S	[0] 
-method_limits 	S	[0] 
-method        	S	[0] 
-lib           	S	[0] 
-profile       	S	[0] 
-profile1      	S	[0] 
-profile2      	S	[0] 
-pdb           	S	[0] 
-relax_lib     	D	[0] 	1 
-filter_lib    	D	[0] 	0 
-shrink_lib    	D	[0] 	0 
-out_lib       	W_F	[0] 	no
-out_lib_mode  	S	[0] 	primary
-lib_only      	D	[0] 	0 
-outseqweight  	W_F	[0] 	no
-dpa           	FL	[0] 	0
-seq_source    	S	[0] 	ANY
-cosmetic_penalty	D	[0] 	0 
-gapopen       	D	[0] 	0 
-gapext        	D	[0] 	0 
-fgapopen      	D	[0] 	0 
-fgapext       	D	[0] 	0 
-nomatch       	D	[0] 	0 
-newtree       	W_F	[0] 	default
-tree          	W_F	[0] 	NO
-usetree       	R_F	[0] 
-tree_mode     	S	[0] 	nj
-distance_matrix_mode	S	[0] 	ktup
-distance_matrix_sim_mode	S	[0] 	idmat_sim1
-quicktree     	FL	[0] 	0
-outfile       	W_F	[0] 	default
-maximise      	FL	[1] 	1
-output        	S	[1] 	score_ascii	html	score_ascii
-len           	D	[0] 	0 
-infile        	R_F	[1] 	/opt/ADOPS/443/Zip48C-PA/batch/allfiles/tcoffee/input.fasta.prot.fasta.clustalw2_rs_0_0.fasta.aln
-matrix        	S	[0] 	default
-tg_mode       	D	[0] 	1 
-profile_mode  	S	[0] 	cw_profile_profile
-profile_comparison	S	[0] 	profile
-dp_mode       	S	[0] 	linked_pair_wise
-ktuple        	D	[0] 	1 
-ndiag         	D	[0] 	0 
-diag_threshold	D	[0] 	0 
-diag_mode     	D	[0] 	0 
-sim_matrix    	S	[0] 	vasiliky
-transform     	S	[0] 
-extend_seq    	FL	[0] 	0
-outorder      	S	[0] 	input
-inorder       	S	[0] 	aligned
-seqnos        	S	[0] 	off
-case          	S	[0] 	keep
-cpu           	D	[0] 	0 
-maxnseq       	D	[0] 	1000 
-maxlen        	D	[0] 	-1 
-sample_dp     	D	[0] 	0 
-weight        	S	[0] 	defa