--- EXPERIMENT NOTES
--- EXPERIMENT PROPERTIES
#Fri Jun 15 18:32:45 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_3/input.fasta
input.names=
mrbayes.params=
codeml.params=
--- PSRF SUMMARY
Estimated marginal likelihoods for runs sampled in files
"/opt/ADOPS1/DNG_A2/prM_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A2/prM_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.lstat)
Run Arithmetic mean Harmonic mean
--------------------------------------
1 -4165.53 -4211.56
2 -4166.14 -4215.63
--------------------------------------
TOTAL -4165.79 -4214.95
--------------------------------------
Model parameter summaries over the runs sampled in files
"/opt/ADOPS1/DNG_A2/prM_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.run1.p" and "/opt/ADOPS1/DNG_A2/prM_3/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_3/batch/allfiles/mrbayes/input.fasta.fasta.mrb.pstat".
95% HPD Interval
--------------------
Parameter Mean Variance Lower Upper Median min ESS* avg ESS PSRF+
------------------------------------------------------------------------------------------------------
TL{all} 5.742301 0.201819 4.869434 6.653942 5.721698 758.64 818.32 1.000
r(A<->C){all} 0.041529 0.000080 0.025394 0.059846 0.041021 547.20 601.50 1.000
r(A<->G){all} 0.238438 0.000694 0.185056 0.287795 0.237011 459.99 511.54 1.000
r(A<->T){all} 0.065939 0.000122 0.044152 0.087205 0.065695 801.06 839.76 1.000
r(C<->G){all} 0.026804 0.000053 0.013541 0.041362 0.026183 763.74 842.33 1.000
r(C<->T){all} 0.594531 0.000981 0.534584 0.657250 0.596150 436.45 492.96 1.000
r(G<->T){all} 0.032759 0.000077 0.015907 0.050031 0.031907 872.85 901.57 1.002
pi(A){all} 0.291144 0.000225 0.260822 0.319138 0.291006 676.18 683.20 1.001
pi(C){all} 0.247681 0.000185 0.222041 0.274805 0.247641 731.41 798.71 1.000
pi(G){all} 0.244790 0.000220 0.215425 0.272958 0.244327 719.12 719.31 1.001
pi(T){all} 0.216385 0.000159 0.190977 0.240499 0.215979 673.00 719.93 1.000
alpha{1,2} 0.214912 0.000381 0.176266 0.253273 0.213274 1154.03 1209.85 1.000
alpha{3} 4.045538 0.812981 2.479430 5.866412 3.946351 1280.86 1388.32 1.000
pinvar{all} 0.081278 0.001171 0.011896 0.143467 0.080782 909.67 1155.05 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 -3982.45163
Model 2: PositiveSelection -3982.45163
Model 0: one-ratio -4025.939801
Model 3: discrete -3943.785617
Model 7: beta -3943.987698
Model 8: beta&w>1 -3943.987969
Model 0 vs 1 86.97634199999993
Model 2 vs 1 0.0
Model 8 vs 7 5.419999997684499E-4
>C1
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITETEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVTALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C2
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVMALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C3
FHLTSRDGEPRMIVAKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWVLRHPGFTILALFLAHYIGTSLTQ
KVVVFTLLMLVTPSMT
>C4
FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RALILILLTAVAPSMT
>C5
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTLT
YKCPRITEVEPDDVDCWCNTTDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRAETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C6
FHLTTRGGEPHMIVSKQERGKSLLFKTSVGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C7
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFMLLMLVTPSMT
>C8
FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHVIGTSITQ
KGIIFILLMLVTPSMA
>C9
FHLTTRNGEPHMIVGIQEKGKSLLFKTENGVNMCTLMAMDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RALIFILLTAVAPSMA
>C10
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPFIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFVLLMLVTPSMA
>C11
FHLTIRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEFCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C12
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRISEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C13
FHLTTRNGEPHMIVSRQEKGKSLLFKTKDGTNMCTLMAMDLGELCEDTIT
YKCPFLKQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRRGKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RVLIFILLTAIAPSMT
>C14
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHTIGTSITQ
KGIIFILLMLVTPSMA
>C15
FHLTSRDGEPRMIVAKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFVLLMLVTPSMT
>C16
FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTIGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RALIFILLTAVAPSMT
>C17
FHLTTRNGEPHMIVSKHEKGKSLLFKTEDGMNMCTLMAMDLGELCEDTIT
YKCPFLKQNEPEDIDCWCNATSTWVTYGTCSTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKQAQRIETWILRHPGFTLMAAILAYTIGTTHFQ
KILIFILLTAVAPSMT
>C18
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGINMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVTALFLAHAIGTSITQ
KGIIFILLILVTPSMA
>C19
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGEICEDTMT
YKCPRITEAEPNHVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALALHEG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C20
FHLTTRNGEPHMIVSIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RALIFILLTAVAPSMT
>C21
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTVT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAHTIGTTYFQ
RVLIFILLTAVAPSMT
>C22
FHLTTRGGEPHMIVSKQERGKSLLFKTSTGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQKVETWALRHPGFTVIAFFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C23
FHLTTRGGEPHMIVSKHERGKALLFKTSTGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C24
FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIVFILLMLVTPSMA
>C25
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLVAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C26
FHLTTRGGEPHMIVTKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSRTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C27
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDAWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C28
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTVT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQ
RVLIFILLTAVAPSMT
>C29
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTMIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C30
FHLTSRDGEPHMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGERRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMT
>C31
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIALFLAHAIGTSITQ
KGTIFILLMLATPSMA
>C32
FHLTSRNGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMT
>C33
FHLTTRNGEPHMIVGRQEKGKSLLFKTEDGVNMCTLMAIDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHVQRIETWILRHPGFTIMAAILANTIGTTHFQ
RALIFILLTAVAPSMT
>C34
FHLTTRGGEPHMIVGKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C35
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMA
>C36
FHLTTRNGEPHMIVSMQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTHFQ
RALIFILLTAVAPSMT
>C37
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTAPGDHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAAILAYTIGTTYFQ
RVLILILLTAVAPSMT
>C38
FHLTSRDGEPRMIVGKNERGKTLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMT
>C39
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPRITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRREKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIAFFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C40
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFAIMAAILAYTIGTTHFQ
RVLIFILLTAVAPSMT
>C41
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVIAFFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C42
FHLTTRNGEPHMIVSRQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YNCPLLRQNEPEDIDCWCNSTSTWVTYGTCTATGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTVMAAILAYTIGTTYFQ
RVLIFILLTAVAPSMT
>C43
FHLTTRGGEPHMIVGKQERGKSLLFKTSAGVNMCTLIAMDLGELCDDTMT
YKCPRITETEPDDVDCWCNATETWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWRQIQKVETWALRHPGFTVIALFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C44
FHLTSRDGEPRMIVGKNERGKSLLFKTATGINMCTLIAMDLGEMCDDTVT
YKCPLIAEVEPEDIDCWCNLTSAWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLIQ
KVVIFILLMLVTPSMT
>C45
FHLTTRGGEPHMIVSKQERGKSLLFKTSAGVNMCTLIAMDLGELCEDTMT
YKCPQITEAEPDDVDCWCNATDTWVTYGTCSQTGEHRRDKRSVALAPHVG
LGLETRTETWMSSEGAWKQIQRVETWALRHPGFTVVAFFLAHAIGTSITQ
KGIIFILLMLVTPSMA
>C46
FHLTTRNGEPHMIVGIQEKGKSLLFKTEDGVNMCTLMAMDLGELCEDTIT
YKCPLLRQNEPEDIDCWCNSTSTWVTYGTCTTTGEHRREKRSVALVPHVG
MGLETRTETWMSSEGAWKHAQRIETWILRHPGFTIMAVILAYTIGTTHFQ
RVLIFILLTAVAPSMT
>C47
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFTLLMLVTPSMT
>C48
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YRCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFTLLMLVTPSMT
>C49
FHLTSRDGEPRMIVGKNERGKSLLFKTASGINMCTLIAMDLGEMCDDTVT
YKCPHITEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVAIAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQ
KVVIFILLMLVTPSMT
>C50
FHLTSRDGEPRMIVGKNERGKSLLFKTATGINMCTLIAMDLGEMCDDTVT
YKCPLIAEVEPEDIDCWCNLTSTWVTYGTCNQAGEHRRDKRSVALAPHVG
MGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLIQ
KVVIFILLMLVTPSMT
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] 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
-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] 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]
