
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:11 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4723.phylip" (19 taxa, 640 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: HKYG


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
HKYG	40	-3156.0269	6397.5297	0.9962	0.9962
HKYIG	41	-3160.6183	6408.9958	0.0032	0.9994
GTRG	44	-3159.3139	6413.2833	0.0004	0.9998
GTRIG	45	-3158.9198	6414.8093	0.0002	1.0000
HKYI	40	-3168.8131	6423.1020	0.0000	1.0000
GTRI	44	-3168.1713	6430.9980	0.0000	1.0000
K2PG	37	-3183.7126	6446.0963	0.0000	1.0000
K2PIG	38	-3187.2519	6455.4356	0.0000	1.0000
SYMG	41	-3186.4032	6460.5655	0.0000	1.0000
SYMIG	42	-3185.4086	6460.8675	0.0000	1.0000
K2PI	37	-3193.7596	6466.1902	0.0000	1.0000
SYMI	41	-3192.0282	6471.8155	0.0000	1.0000
HKY	39	-3239.9558	6563.1116	0.0000	1.0000
GTR	43	-3244.5015	6581.3520	0.0000	1.0000
K2P	36	-3267.4016	6611.2211	0.0000	1.0000
F81G	39	-3268.5521	6620.3042	0.0000	1.0000
F81IG	40	-3267.6932	6620.8622	0.0000	1.0000
SYM	40	-3271.5792	6628.6342	0.0000	1.0000
F81I	39	-3273.5652	6630.3303	0.0000	1.0000
JC69G	36	-3285.3435	6647.1050	0.0000	1.0000
JC69IG	37	-3284.3162	6647.3035	0.0000	1.0000
JC69I	36	-3289.8645	6656.1469	0.0000	1.0000
F81	38	-3346.4286	6773.7889	0.0000	1.0000
JC69	35	-3358.9852	6792.1426	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-3156.0269	6392.0539	0.9952	0.9952
HKYIG	41	-3160.6183	6403.2366	0.0037	0.9989
GTRG	44	-3159.3139	6406.6278	0.0007	0.9996
GTRIG	45	-3158.9198	6407.8396	0.0004	1.0000
HKYI	40	-3168.8131	6417.6262	0.0000	1.0000
GTRI	44	-3168.1713	6424.3425	0.0000	1.0000
K2PG	37	-3183.7126	6441.4252	0.0000	1.0000
K2PIG	38	-3187.2519	6450.5038	0.0000	1.0000
SYMG	41	-3186.4032	6454.8063	0.0000	1.0000
SYMIG	42	-3185.4086	6454.8172	0.0000	1.0000
K2PI	37	-3193.7596	6461.5191	0.0000	1.0000
SYMI	41	-3192.0282	6466.0563	0.0000	1.0000
HKY	39	-3239.9558	6557.9116	0.0000	1.0000
GTR	43	-3244.5015	6575.0030	0.0000	1.0000
K2P	36	-3267.4016	6606.8032	0.0000	1.0000
F81G	39	-3268.5521	6615.1042	0.0000	1.0000
F81IG	40	-3267.6932	6615.3864	0.0000	1.0000
SYM	40	-3271.5792	6623.1584	0.0000	1.0000
F81I	39	-3273.5652	6625.1303	0.0000	1.0000
JC69IG	37	-3284.3162	6642.6324	0.0000	1.0000
JC69G	36	-3285.3435	6642.6870	0.0000	1.0000
JC69I	36	-3289.8645	6651.7289	0.0000	1.0000
F81	38	-3346.4286	6768.8571	0.0000	1.0000
JC69	35	-3358.9852	6787.9705	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3156.0269	6570.5126	0.9996	0.9996
HKYIG	41	-3160.6183	6586.1568	0.0004	1.0000
HKYI	40	-3168.8131	6596.0849	0.0000	1.0000
GTRG	44	-3159.3139	6602.9324	0.0000	1.0000
K2PG	37	-3183.7126	6606.4995	0.0000	1.0000
GTRIG	45	-3158.9198	6608.6057	0.0000	1.0000
K2PIG	38	-3187.2519	6620.0396	0.0000	1.0000
GTRI	44	-3168.1713	6620.6471	0.0000	1.0000
K2PI	37	-3193.7596	6626.5935	0.0000	1.0000
SYMG	41	-3186.4032	6637.7265	0.0000	1.0000
SYMIG	42	-3185.4086	6642.1989	0.0000	1.0000
SYMI	41	-3192.0282	6648.9765	0.0000	1.0000
HKY	39	-3239.9558	6731.9089	0.0000	1.0000
GTR	43	-3244.5015	6766.8461	0.0000	1.0000
K2P	36	-3267.4016	6767.4160	0.0000	1.0000
F81G	39	-3268.5521	6789.1015	0.0000	1.0000
F81IG	40	-3267.6932	6793.8451	0.0000	1.0000
F81I	39	-3273.5652	6799.1276	0.0000	1.0000
SYM	40	-3271.5792	6801.6171	0.0000	1.0000
JC69G	36	-3285.3435	6803.2999	0.0000	1.0000
JC69IG	37	-3284.3162	6807.7067	0.0000	1.0000
JC69I	36	-3289.8645	6812.3418	0.0000	1.0000
F81	38	-3346.4286	6938.3929	0.0000	1.0000
JC69	35	-3358.9852	6944.1218	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4723.phylip = 1 - 640;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4723.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4723.phylip = 1 - 640;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4723.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4723.phylip = 1 - 640;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_4723.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

