
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:43 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_3420.phylip" (19 taxa, 417 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	-1482.9789	3054.6813	0.5139	0.5139
HKYIG	41	-1482.9698	3057.1236	0.1515	0.6654
HKYI	40	-1484.4042	3057.5318	0.1236	0.7890
GTRIG	45	-1478.4339	3058.0268	0.0965	0.8855
GTRI	44	-1480.1806	3059.0064	0.0591	0.9446
GTRG	44	-1480.2450	3059.1351	0.0554	1.0000
HKY	39	-1496.2496	3078.7750	0.0000	1.0000
K2PG	37	-1499.1779	3079.7752	0.0000	1.0000
K2PIG	38	-1499.1707	3082.1827	0.0000	1.0000
F81IG	40	-1496.7471	3082.2176	0.0000	1.0000
K2PI	37	-1500.6204	3082.6604	0.0000	1.0000
F81I	39	-1498.1996	3082.6750	0.0000	1.0000
GTR	43	-1493.2794	3082.7035	0.0000	1.0000
F81G	39	-1499.2663	3084.8085	0.0000	1.0000
SYMIG	42	-1498.1921	3090.0420	0.0000	1.0000
SYMG	41	-1500.2899	3091.7638	0.0000	1.0000
SYMI	41	-1500.9364	3093.0568	0.0000	1.0000
JC69IG	37	-1510.8068	3103.0331	0.0000	1.0000
K2P	36	-1512.3989	3103.8083	0.0000	1.0000
JC69G	36	-1513.2935	3105.5976	0.0000	1.0000
F81	38	-1511.2700	3106.3813	0.0000	1.0000
JC69I	36	-1514.0313	3107.0731	0.0000	1.0000
SYM	40	-1512.1867	3113.0969	0.0000	1.0000
JC69	35	-1525.2946	3127.2034	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1482.9789	3045.9579	0.3535	0.3535
GTRIG	45	-1478.4339	3046.8678	0.2243	0.5778
HKYIG	41	-1482.9698	3047.9396	0.1312	0.7090
GTRI	44	-1480.1806	3048.3613	0.1063	0.8153
GTRG	44	-1480.2450	3048.4900	0.0997	0.9150
HKYI	40	-1484.4042	3048.8084	0.0850	1.0000
HKY	39	-1496.2496	3070.4992	0.0000	1.0000
K2PG	37	-1499.1779	3072.3557	0.0000	1.0000
GTR	43	-1493.2794	3072.5587	0.0000	1.0000
F81IG	40	-1496.7471	3073.4942	0.0000	1.0000
K2PIG	38	-1499.1707	3074.3415	0.0000	1.0000
F81I	39	-1498.1996	3074.3991	0.0000	1.0000
K2PI	37	-1500.6204	3075.2408	0.0000	1.0000
F81G	39	-1499.2663	3076.5326	0.0000	1.0000
SYMIG	42	-1498.1921	3080.3842	0.0000	1.0000
SYMG	41	-1500.2899	3082.5798	0.0000	1.0000
SYMI	41	-1500.9364	3083.8728	0.0000	1.0000
JC69IG	37	-1510.8068	3095.6136	0.0000	1.0000
K2P	36	-1512.3989	3096.7978	0.0000	1.0000
F81	38	-1511.2700	3098.5400	0.0000	1.0000
JC69G	36	-1513.2935	3098.5870	0.0000	1.0000
JC69I	36	-1514.0313	3100.0626	0.0000	1.0000
SYM	40	-1512.1867	3104.3735	0.0000	1.0000
JC69	35	-1525.2946	3120.5892	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1482.9789	3207.2813	0.7745	0.7745
HKYI	40	-1484.4042	3210.1319	0.1862	0.9607
HKYIG	41	-1482.9698	3213.2962	0.0383	0.9990
K2PG	37	-1499.1779	3221.5799	0.0006	0.9996
K2PI	37	-1500.6204	3224.4650	0.0001	0.9998
GTRI	44	-1480.1806	3225.8171	0.0001	0.9998
GTRG	44	-1480.2450	3225.9458	0.0001	0.9999
K2PIG	38	-1499.1707	3227.5987	0.0000	0.9999
HKY	39	-1496.2496	3227.7895	0.0000	1.0000
GTRIG	45	-1478.4339	3228.3566	0.0000	1.0000
F81I	39	-1498.1996	3231.6895	0.0000	1.0000
F81G	39	-1499.2663	3233.8230	0.0000	1.0000
F81IG	40	-1496.7471	3234.8176	0.0000	1.0000
K2P	36	-1512.3989	3241.9889	0.0000	1.0000
JC69G	36	-1513.2935	3243.7781	0.0000	1.0000
JC69IG	37	-1510.8068	3244.8378	0.0000	1.0000
JC69I	36	-1514.0313	3245.2537	0.0000	1.0000
GTR	43	-1493.2794	3245.9814	0.0000	1.0000
SYMG	41	-1500.2899	3247.9363	0.0000	1.0000
SYMI	41	-1500.9364	3249.2293	0.0000	1.0000
SYMIG	42	-1498.1921	3249.7739	0.0000	1.0000
F81	38	-1511.2700	3251.7973	0.0000	1.0000
JC69	35	-1525.2946	3261.7472	0.0000	1.0000
SYM	40	-1512.1867	3265.6969	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_3420.phylip = 1 - 417;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3420.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_3420.phylip = 1 - 417;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3420.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_3420.phylip = 1 - 417;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3420.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

