
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:22 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/chr5_1698.phylip" (19 taxa, 434 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1481.2726	3060.7251	0.5823	0.5823
GTRIG	45	-1480.4390	3061.5481	0.3859	0.9682
HKYG	40	-1489.9671	3068.2804	0.0133	0.9815
GTRI	44	-1485.1628	3068.5055	0.0119	0.9934
HKYIG	41	-1489.5059	3069.7975	0.0062	0.9996
HKYI	40	-1493.5140	3075.3741	0.0004	1.0000
K2PG	37	-1502.9208	3086.9426	0.0000	1.0000
K2PIG	38	-1502.6024	3088.7087	0.0000	1.0000
SYMG	41	-1500.4798	3091.7454	0.0000	1.0000
SYMIG	42	-1499.9865	3093.2108	0.0000	1.0000
K2PI	37	-1506.1078	3093.3167	0.0000	1.0000
SYMI	41	-1503.0557	3096.8970	0.0000	1.0000
GTR	43	-1525.0081	3145.7187	0.0000	1.0000
HKY	39	-1533.5988	3153.1164	0.0000	1.0000
F81G	39	-1538.6556	3163.2301	0.0000	1.0000
F81IG	40	-1538.4205	3165.1870	0.0000	1.0000
F81I	39	-1542.5006	3170.9200	0.0000	1.0000
K2P	36	-1546.6725	3172.0553	0.0000	1.0000
SYM	40	-1542.7917	3173.9294	0.0000	1.0000
JC69G	36	-1547.8548	3174.4199	0.0000	1.0000
JC69IG	37	-1547.6085	3176.3179	0.0000	1.0000
JC69I	36	-1551.8886	3182.4875	0.0000	1.0000
F81	38	-1580.8385	3245.1809	0.0000	1.0000
JC69	35	-1590.3936	3257.1189	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1481.2726	3050.5452	0.5314	0.5314
GTRIG	45	-1480.4390	3050.8780	0.4499	0.9813
GTRI	44	-1485.1628	3058.3256	0.0109	0.9922
HKYG	40	-1489.9671	3059.9343	0.0049	0.9970
HKYIG	41	-1489.5059	3061.0118	0.0028	0.9999
HKYI	40	-1493.5140	3067.0280	0.0001	1.0000
K2PG	37	-1502.9208	3079.8416	0.0000	1.0000
K2PIG	38	-1502.6024	3081.2049	0.0000	1.0000
SYMG	41	-1500.4798	3082.9596	0.0000	1.0000
SYMIG	42	-1499.9865	3083.9729	0.0000	1.0000
K2PI	37	-1506.1078	3086.2156	0.0000	1.0000
SYMI	41	-1503.0557	3088.1113	0.0000	1.0000
GTR	43	-1525.0081	3136.0162	0.0000	1.0000
HKY	39	-1533.5988	3145.1976	0.0000	1.0000
F81G	39	-1538.6556	3155.3113	0.0000	1.0000
F81IG	40	-1538.4205	3156.8409	0.0000	1.0000
F81I	39	-1542.5006	3163.0012	0.0000	1.0000
K2P	36	-1546.6725	3165.3450	0.0000	1.0000
SYM	40	-1542.7917	3165.5833	0.0000	1.0000
JC69G	36	-1547.8548	3167.7096	0.0000	1.0000
JC69IG	37	-1547.6085	3169.2169	0.0000	1.0000
JC69I	36	-1551.8886	3175.7772	0.0000	1.0000
F81	38	-1580.8385	3237.6771	0.0000	1.0000
JC69	35	-1590.3936	3250.7873	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1489.9671	3222.8561	0.8587	0.8587
HKYIG	41	-1489.5059	3228.0066	0.0654	0.9241
GTRG	44	-1481.2726	3229.7591	0.0272	0.9513
HKYI	40	-1493.5140	3229.9498	0.0247	0.9761
K2PG	37	-1502.9208	3230.5443	0.0184	0.9945
GTRIG	45	-1480.4390	3234.1650	0.0030	0.9975
K2PIG	38	-1502.6024	3235.9806	0.0012	0.9987
K2PI	37	-1506.1078	3236.9183	0.0008	0.9994
GTRI	44	-1485.1628	3237.5395	0.0006	1.0000
SYMG	41	-1500.4798	3249.9545	0.0000	1.0000
SYMIG	42	-1499.9865	3255.0408	0.0000	1.0000
SYMI	41	-1503.0557	3255.1061	0.0000	1.0000
HKY	39	-1533.5988	3304.0464	0.0000	1.0000
GTR	43	-1525.0081	3311.1571	0.0000	1.0000
K2P	36	-1546.6725	3311.9746	0.0000	1.0000
F81G	39	-1538.6556	3314.1600	0.0000	1.0000
JC69G	36	-1547.8548	3314.3392	0.0000	1.0000
F81IG	40	-1538.4205	3319.7627	0.0000	1.0000
JC69IG	37	-1547.6085	3319.9196	0.0000	1.0000
F81I	39	-1542.5006	3321.8500	0.0000	1.0000
JC69I	36	-1551.8886	3322.4068	0.0000	1.0000
SYM	40	-1542.7917	3328.5051	0.0000	1.0000
F81	38	-1580.8385	3392.4528	0.0000	1.0000
JC69	35	-1590.3936	3393.3438	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1698.phylip = 1 - 434;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1698.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1698.phylip = 1 - 434;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1698.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) 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/chr5_1698.phylip = 1 - 434;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1698.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

