
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:36 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_8428.phylip" (19 taxa, 376 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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	-1470.7889	3031.3688	0.6220	0.6220
HKYIG	41	-1470.5836	3033.4787	0.2166	0.8386
K2PG	37	-1476.3992	3035.1180	0.0954	0.9340
K2PIG	38	-1476.1531	3037.1014	0.0354	0.9694
HKYI	40	-1474.6447	3039.0805	0.0132	0.9826
GTRG	44	-1469.7530	3039.4698	0.0108	0.9934
GTRIG	45	-1469.5591	3041.6637	0.0036	0.9970
K2PI	37	-1480.4836	3043.2867	0.0016	0.9987
SYMG	41	-1476.1663	3044.6440	0.0008	0.9995
SYMIG	42	-1475.9123	3046.6715	0.0003	0.9998
GTRI	44	-1473.6403	3047.2443	0.0002	1.0000
SYMI	41	-1480.3313	3052.9739	0.0000	1.0000
F81G	39	-1491.3468	3069.9794	0.0000	1.0000
JC69G	36	-1495.9992	3071.8567	0.0000	1.0000
F81IG	40	-1491.1562	3072.1034	0.0000	1.0000
JC69IG	37	-1495.7815	3073.8825	0.0000	1.0000
F81I	39	-1495.2695	3077.8248	0.0000	1.0000
JC69I	36	-1500.0693	3079.9971	0.0000	1.0000
HKY	39	-1500.4390	3088.1637	0.0000	1.0000
K2P	36	-1506.4884	3092.8351	0.0000	1.0000
GTR	43	-1499.2445	3095.8866	0.0000	1.0000
SYM	40	-1506.0814	3101.9538	0.0000	1.0000
F81	38	-1519.7920	3124.3792	0.0000	1.0000
JC69	35	-1524.7229	3126.8575	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1470.7889	3021.5778	0.6023	0.6023
HKYIG	41	-1470.5836	3023.1673	0.2720	0.8743
K2PG	37	-1476.3992	3026.7985	0.0443	0.9186
GTRG	44	-1469.7530	3027.5060	0.0311	0.9496
K2PIG	38	-1476.1531	3028.3061	0.0208	0.9705
GTRIG	45	-1469.5591	3029.1183	0.0139	0.9844
HKYI	40	-1474.6447	3029.2895	0.0127	0.9971
SYMG	41	-1476.1663	3034.3326	0.0010	0.9981
K2PI	37	-1480.4836	3034.9672	0.0007	0.9989
GTRI	44	-1473.6403	3035.2806	0.0006	0.9995
SYMIG	42	-1475.9123	3035.8247	0.0005	1.0000
SYMI	41	-1480.3313	3042.6626	0.0000	1.0000
F81G	39	-1491.3468	3060.6936	0.0000	1.0000
F81IG	40	-1491.1562	3062.3124	0.0000	1.0000
JC69G	36	-1495.9992	3063.9983	0.0000	1.0000
JC69IG	37	-1495.7815	3065.5629	0.0000	1.0000
F81I	39	-1495.2695	3068.5391	0.0000	1.0000
JC69I	36	-1500.0693	3072.1387	0.0000	1.0000
HKY	39	-1500.4390	3078.8780	0.0000	1.0000
GTR	43	-1499.2445	3084.4890	0.0000	1.0000
K2P	36	-1506.4884	3084.9767	0.0000	1.0000
SYM	40	-1506.0814	3092.1627	0.0000	1.0000
F81	38	-1519.7920	3115.5840	0.0000	1.0000
JC69	35	-1524.7229	3119.4457	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1476.3992	3172.1933	0.8901	0.8901
K2PIG	38	-1476.1531	3177.6305	0.0587	0.9488
HKYG	40	-1470.7889	3178.7613	0.0334	0.9822
K2PI	37	-1480.4836	3180.3620	0.0150	0.9972
HKYIG	41	-1470.5836	3184.2804	0.0021	0.9993
HKYI	40	-1474.6447	3186.4730	0.0007	1.0000
SYMG	41	-1476.1663	3195.4458	0.0000	1.0000
GTRG	44	-1469.7530	3200.4079	0.0000	1.0000
SYMIG	42	-1475.9123	3200.8674	0.0000	1.0000
SYMI	41	-1480.3313	3203.7757	0.0000	1.0000
JC69G	36	-1495.9992	3205.4635	0.0000	1.0000
GTRIG	45	-1469.5591	3205.9498	0.0000	1.0000
GTRI	44	-1473.6403	3208.1825	0.0000	1.0000
JC69IG	37	-1495.7815	3210.9577	0.0000	1.0000
JC69I	36	-1500.0693	3213.6039	0.0000	1.0000
F81G	39	-1491.3468	3213.9476	0.0000	1.0000
F81IG	40	-1491.1562	3219.4959	0.0000	1.0000
F81I	39	-1495.2695	3221.7931	0.0000	1.0000
K2P	36	-1506.4884	3226.4419	0.0000	1.0000
HKY	39	-1500.4390	3232.1320	0.0000	1.0000
SYM	40	-1506.0814	3249.3463	0.0000	1.0000
GTR	43	-1499.2445	3253.4613	0.0000	1.0000
JC69	35	-1524.7229	3256.9814	0.0000	1.0000
F81	38	-1519.7920	3264.9083	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/chr1_8428.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8428.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/chr1_8428.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8428.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8428.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_8428.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

