--- EXPERIMENT NOTES




 --- EXPERIMENT PROPERTIES

#Fri Jun 15 11:41:58 WEST 2018
codeml.models=0 1 2 3 7 8
mrbayes.mpich=
mrbayes.ngen=1000000
tcoffee.alignMethod=MUSCLE
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/ADOPS1/DNG_A2/prM_2/input.fasta
input.names=
mrbayes.params=
codeml.params=



 --- PSRF SUMMARY

      Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_A2/prM_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A2/prM_2/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/ADOPS1/DNG_A2/prM_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)

Run   Arithmetic mean   Harmonic mean
--------------------------------------
1      -4701.63         -4742.00
2      -4699.84         -4743.19
--------------------------------------
TOTAL    -4700.38         -4742.77
--------------------------------------


Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_A2/prM_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A2/prM_2/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/ADOPS1/DNG_A2/prM_2/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".

95% HPD Interval
--------------------
Parameter         Mean      Variance     Lower       Upper       Median    min ESS*  avg ESS    PSRF+
------------------------------------------------------------------------------------------------------
TL{all}         6.817570    0.234939    5.887452    7.753037    6.798747    820.17    921.59    1.000
r(A<->C){all}   0.046487    0.000068    0.031626    0.064081    0.046098    714.13    833.84    1.000
r(A<->G){all}   0.215933    0.000511    0.176201    0.263121    0.214815    358.44    417.62    1.000
r(A<->T){all}   0.063403    0.000107    0.044258    0.085426    0.062899    641.13    798.93    1.000
r(C<->G){all}   0.032301    0.000061    0.017213    0.047337    0.031899    877.60    928.98    1.000
r(C<->T){all}   0.595068    0.000796    0.539118    0.647069    0.595721    386.46    416.41    1.000
r(G<->T){all}   0.046808    0.000105    0.026663    0.066281    0.046359    864.76    925.37    1.000
pi(A){all}      0.312011    0.000217    0.284018    0.341832    0.311854    681.56    760.65    1.000
pi(C){all}      0.240456    0.000176    0.214938    0.266175    0.240508    747.38    818.21    1.000
pi(G){all}      0.235204    0.000199    0.209133    0.263719    0.234504    699.16    741.38    1.000
pi(T){all}      0.212329    0.000143    0.189284    0.236008    0.212210    720.68    770.12    1.000
alpha{1,2}      0.232069    0.000401    0.193795    0.271750    0.230159   1207.98   1312.33    1.000
alpha{3}        4.215188    0.848041    2.602160    6.121293    4.103657   1190.52   1255.03    1.000
pinvar{all}     0.069274    0.000824    0.015642    0.124458    0.067762   1257.94   1350.86    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	-4487.900608
Model 2: PositiveSelection	-4487.900667
Model 0: one-ratio	-4527.821913
Model 3: discrete	-4450.722062
Model 7: beta	-4455.85967
Model 8: beta&w>1	-4455.859693


Model 0 vs 1	79.8426099999997

Model 2 vs 1	1.1799999992945231E-4

Model 8 vs 7	4.600000102072954E-5
>C1
FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT
YKCPLLVNTEPEDIDCWCNLTATWVMYGTCTQSGERRREKRSVALTPHSG
MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ
RTVFFVLMMLVAPSYG
>C2
FHLTTRGGEPHMIVSKQERGKSLLFKTPAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C3
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSTEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMT
>C4
FSLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT
YKCPLLVNTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSG
MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ
RTVFFVLMMLVAPSYG
>C5
FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTAPGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAGKHAQRIETWVLRHPGFTIMAAILAYTIGTTYFQ
RVLIFILLTAVTPSMT
>C6
FSLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT
YKCPLLVNTEPEDIDCWCNLTSAWVMYGTCTQSGERRREKRSVALTPHSG
MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ
RTVFFILMMLVAPSYG
>C7
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRISEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C8
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C9
FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWVLRHPGFTIMAAILAYTIGTTYFQ
RVLIFILLTTVAPSMT
>C10
FHLTTRNGEPHMIVSIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RVLIFILLTAVAPSMT
>C11
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRTRRHRLYGG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQ
RVLIFILLTAVAPSMT
>C12
FHLTTRGGEPHMIVGKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C13
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITETEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSTTQ
KGIIFILLMLVTPSMA
>C14
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGINMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVTALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C15
FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEVEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHVIGTSITQ
KGIIFILLMLVTPSMA
>C16
FHLTTRGGEPHMIVSKQERGKSLLFKTSGGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C17
FHLSTRDGEPLMIVAKHERGRPLLFKTTEGINKCTLIAMDLGEMCEDTVT
YKCPLLINTEPEDIDCWCNLTSTWVMYGTCTQSGERRREKRSVALTPHSG
MGLETRAETWMSSEGAWKHAQRVESWILRNPGFALLAGFMAYMIGQTGIQ
RTVFFVLMMLVAPSYG
>C18
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRIAEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFMVIAFFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C19
FHLTTRGGEPHMILSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C20
FHLTTRNGEPHMIVSKNEKGKSLLFKTENGINMCTLMAMDLGELCEDTIT
YKCPFLKQNEPEDIDCWCNSTSTWVTYGTCSSTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKQAQRIETWILRHPGFTLMAAVLAYTIGTTHFQ
RALIFILLTAVAPSMT
>C21
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCPQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAVGTSITQ
KGIIFILLMLVTPSMA
>C22
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEMEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C23
FHLTTRGGEPHMIVGKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT
YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHVIGTSITQ
KGIIFILLMLVTPSMA
>C24
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQNGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C25
FHLTTREGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C26
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGDMCDDTVT
YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMA
>C27
FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIVFILLMLVTPSMA
>C28
FHLTTRNGEPHMIVSMQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RALIFILLTAVAPSMT
>C29
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YNCPPLQQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQ
RVLIFILLTAVAPSMT
>C30
FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFIIMAAILAYTIGTTHFQ
RALIFILLTAVAPSMT
>C31
FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVTALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C32
FHLTTRNGEPHMIVSRQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALAPHVG
MGLETRTETWMSSEGAWKHAQRIEIWVLRHPGFTIMAAILAYTIGTTYFQ
RVLIFILLTAVAPSMT
>C33
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTIT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMT
>C34
FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHTIGTSITQ
KGIIFILLMLVTPSMA
>C35
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRREKRSVALAPHVG
LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C36
FHLTSRDGEPRMIVGKNERGKTLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMT
>C37
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RALIFILLTAVAPSMT
>C38
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIEIWILRHPGFTIMAAILAYTIGTTHFQ
RALIFILLTAVAPSMT
>C39
FHLTTRGGEPHMVVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGGHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C40
FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ
KALIFILLTAVAPSMT
>C41
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFMLLMLVTPSMT
>C42
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C43
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPLIAEAEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMT
>C44
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSPTQ
KVVIFILLMLVTPSMT
>C45
FHLTTRGGEPHMIVSKQERGKSLLFKTSVGVNMCTLIAMDLGELCEDTMT
YKCPRITEVEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C46
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C47
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCPQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C48
FHLTTRDGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ
KALIFILLTAVAPSMT
>C49
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLIQ
KVVIFVLLMLVTPSMT
>C50
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGGHRREKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA

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
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-seq_name_for_quadruplet	S	[0] 	all
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-clean         	S	[0] 	no
-do_self       	FL	[0] 	0
-do_normalise  	D	[0] 	1000 
-template_file 	S	[0] 
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-template_mode 	S	[0] 
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-remove_template_file	D	[0] 	0 
-profile_template_file	S	[0] 
-in            	S	[0] 
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-aln           	S	[0] 
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-outseqweight  	W_F	[0] 	no
-dpa           	FL	[0] 	0
-seq_source    	S	[0] 	ANY
-cosmetic_penalty	D	[0] 	0 
-gapopen       	D	[0] 	0 
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-fgapopen      	D	[0] 	0 
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-usetree       	R_F	[0] 
-tree_mode     	S	[0] 	nj
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-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] 	input.prot.fasta.muscle_rs_0_0.fasta.aln
-matrix        	S	[0] 	default
-tg_mode       	D	[0] 	1 
-profile_mode  	S	[0] 	cw_profile_profile
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-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] 	default
-seq_weight    	S	[0] 	no
-align         	FL	[1] 	1
-mocca         	FL	[0] 	0
-domain        	FL	[0] 	0
-start         	D	[0] 	0 
-len           	D	[0] 	0 
-scale         	D	[0] 	0 
-mocca_interactive	FL	[0] 	0
-method_evaluate_mode	S	[0] 	default
-evaluate_mode 	S	[1] 	t_coffee_fast
-get_type      	FL	[0] 	0
-clean_aln     	D	[0] 	0 
-clean_threshold	D	[1] 	1 
-clean_iteration	D	[1] 	1 
-clean_evaluate_mode	S	[0] 	t_coffee_fast
-extend_matrix 	FL	[0] 	0
-prot_min_sim  	D	[40] 	40 
-prot_max_sim  	D	[90] 	90 
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair 

Identify Master Sequences [no]:

Master Sequences Identified
INPUT SEQUENCES: 50 SEQUENCES  [PROTEIN]
	Multi Core Mode: 72 processors:

	--- Process Method/Library/Aln Sinput.prot.fasta.muscle_rs_0_0.fasta.aln
-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) input.prot.fasta.muscle_rs_0_0.fasta.aln  Format clustal_aln
	Input File (M) proba_pair