--- 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 