
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:24 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/chr1_34773.phylip" (19 taxa, 404 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: K2PI


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
HKYI	40	-1557.9411	3204.9180	0.4136	0.4136
HKYG	40	-1558.1264	3205.2886	0.3436	0.7571
HKYIG	41	-1557.9242	3207.3621	0.1218	0.8790
K2PI	37	-1563.8987	3209.4805	0.0422	0.9212
K2PG	37	-1563.9819	3209.6469	0.0389	0.9601
K2PIG	38	-1563.8475	3211.8155	0.0131	0.9732
HKY	39	-1563.3689	3213.3091	0.0062	0.9795
GTRI	44	-1557.3725	3213.7757	0.0049	0.9844
GTRG	44	-1557.4666	3213.9638	0.0045	0.9889
SYMI	41	-1561.2846	3214.0831	0.0042	0.9931
SYMG	41	-1561.4314	3214.3765	0.0037	0.9968
GTRIG	45	-1557.3338	3216.2318	0.0014	0.9982
SYMIG	42	-1561.2493	3216.5042	0.0013	0.9995
K2P	36	-1569.7731	3218.8050	0.0004	0.9999
GTR	43	-1563.0192	3222.5494	0.0001	1.0000
SYM	40	-1566.9659	3222.9676	0.0000	1.0000
F81I	39	-1596.8248	3280.2211	0.0000	1.0000
F81G	39	-1596.8638	3280.2990	0.0000	1.0000
JC69I	36	-1601.3466	3281.9520	0.0000	1.0000
JC69G	36	-1601.3997	3282.0583	0.0000	1.0000
F81IG	40	-1596.7572	3282.5503	0.0000	1.0000
JC69IG	37	-1601.2868	3284.2566	0.0000	1.0000
F81	38	-1602.2416	3288.6038	0.0000	1.0000
JC69	35	-1606.6998	3290.2475	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1557.9411	3195.8821	0.4097	0.4097
HKYG	40	-1558.1264	3196.2528	0.3404	0.7501
HKYIG	41	-1557.9242	3197.8483	0.1533	0.9033
K2PI	37	-1563.8987	3201.7974	0.0213	0.9246
K2PG	37	-1563.9819	3201.9638	0.0196	0.9442
GTRI	44	-1557.3725	3202.7450	0.0132	0.9575
GTRG	44	-1557.4666	3202.9332	0.0121	0.9695
K2PIG	38	-1563.8475	3203.6950	0.0082	0.9778
SYMI	41	-1561.2846	3204.5693	0.0053	0.9831
GTRIG	45	-1557.3338	3204.6676	0.0051	0.9881
HKY	39	-1563.3689	3204.7377	0.0049	0.9930
SYMG	41	-1561.4314	3204.8627	0.0046	0.9976
SYMIG	42	-1561.2493	3206.4986	0.0020	0.9997
K2P	36	-1569.7731	3211.5462	0.0002	0.9998
GTR	43	-1563.0192	3212.0383	0.0001	1.0000
SYM	40	-1566.9659	3213.9317	0.0000	1.0000
F81I	39	-1596.8248	3271.6497	0.0000	1.0000
F81G	39	-1596.8638	3271.7276	0.0000	1.0000
F81IG	40	-1596.7572	3273.5145	0.0000	1.0000
JC69I	36	-1601.3466	3274.6931	0.0000	1.0000
JC69G	36	-1601.3997	3274.7994	0.0000	1.0000
JC69IG	37	-1601.2868	3276.5736	0.0000	1.0000
F81	38	-1602.2416	3280.4832	0.0000	1.0000
JC69	35	-1606.6998	3283.3997	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-1563.8987	3349.8498	0.4710	0.4710
K2PG	37	-1563.9819	3350.0162	0.4334	0.9045
K2P	36	-1569.7731	3355.5971	0.0266	0.9311
K2PIG	38	-1563.8475	3355.7487	0.0247	0.9557
HKYI	40	-1557.9411	3355.9387	0.0224	0.9782
HKYG	40	-1558.1264	3356.3094	0.0186	0.9968
HKY	39	-1563.3689	3360.7929	0.0020	0.9988
HKYIG	41	-1557.9242	3361.9063	0.0011	0.9999
SYMI	41	-1561.2846	3368.6273	0.0000	1.0000
SYMG	41	-1561.4314	3368.9207	0.0000	1.0000
SYM	40	-1566.9659	3373.9883	0.0000	1.0000
SYMIG	42	-1561.2493	3374.5581	0.0000	1.0000
GTRI	44	-1557.3725	3378.8073	0.0000	1.0000
GTRG	44	-1557.4666	3378.9954	0.0000	1.0000
GTR	43	-1563.0192	3384.0991	0.0000	1.0000
GTRIG	45	-1557.3338	3384.7313	0.0000	1.0000
JC69I	36	-1601.3466	3418.7441	0.0000	1.0000
JC69G	36	-1601.3997	3418.8504	0.0000	1.0000
JC69	35	-1606.6998	3423.4492	0.0000	1.0000
JC69IG	37	-1601.2868	3424.6259	0.0000	1.0000
F81I	39	-1596.8248	3427.7049	0.0000	1.0000
F81G	39	-1596.8638	3427.7828	0.0000	1.0000
F81	38	-1602.2416	3432.5370	0.0000	1.0000
F81IG	40	-1596.7572	3433.5711	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34773.phylip = 1 - 404;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34773.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34773.phylip = 1 - 404;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34773.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34773.phylip = 1 - 404;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_34773.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

