
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:43 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/chr5_3342.phylip" (19 taxa, 445 characters)

Minimum AIC  model: GTRG
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	-1364.3672	2816.8533	0.3712	0.3712
GTRG	44	-1360.0726	2818.0452	0.2045	0.5757
HKYI	40	-1365.1891	2818.4970	0.1632	0.7389
HKYIG	41	-1364.2937	2819.1332	0.1187	0.8576
GTRI	44	-1361.0228	2819.9457	0.0791	0.9367
GTRIG	45	-1360.0071	2820.3901	0.0633	1.0000
HKY	39	-1376.7922	2839.2881	0.0000	1.0000
GTR	43	-1372.3360	2840.1084	0.0000	1.0000
F81G	39	-1387.1439	2859.9914	0.0000	1.0000
F81I	39	-1387.7950	2861.2937	0.0000	1.0000
F81IG	40	-1387.0795	2862.2779	0.0000	1.0000
K2PG	37	-1391.2836	2863.4764	0.0000	1.0000
K2PI	37	-1391.9283	2864.7657	0.0000	1.0000
K2PIG	38	-1391.1952	2865.6910	0.0000	1.0000
SYMG	41	-1389.7378	2870.0216	0.0000	1.0000
SYMI	41	-1390.3992	2871.3443	0.0000	1.0000
SYMIG	42	-1389.6546	2872.2942	0.0000	1.0000
F81	38	-1399.8320	2882.9644	0.0000	1.0000
K2P	36	-1404.9205	2888.3703	0.0000	1.0000
SYM	40	-1402.9170	2893.9529	0.0000	1.0000
JC69G	36	-1412.4666	2903.4625	0.0000	1.0000
JC69I	36	-1413.0404	2904.6102	0.0000	1.0000
JC69IG	37	-1412.4017	2905.7125	0.0000	1.0000
JC69	35	-1425.4816	2927.1245	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1360.0726	2808.1452	0.3178	0.3178
HKYG	40	-1364.3672	2808.7345	0.2367	0.5545
GTRIG	45	-1360.0071	2810.0142	0.1248	0.6793
GTRI	44	-1361.0228	2810.0457	0.1229	0.8022
HKYI	40	-1365.1891	2810.3782	0.1041	0.9063
HKYIG	41	-1364.2937	2810.5873	0.0937	1.0000
GTR	43	-1372.3360	2830.6720	0.0000	1.0000
HKY	39	-1376.7922	2831.5844	0.0000	1.0000
F81G	39	-1387.1439	2852.2877	0.0000	1.0000
F81I	39	-1387.7950	2853.5900	0.0000	1.0000
F81IG	40	-1387.0795	2854.1591	0.0000	1.0000
K2PG	37	-1391.2836	2856.5673	0.0000	1.0000
K2PI	37	-1391.9283	2857.8566	0.0000	1.0000
K2PIG	38	-1391.1952	2858.3905	0.0000	1.0000
SYMG	41	-1389.7378	2861.4757	0.0000	1.0000
SYMI	41	-1390.3992	2862.7984	0.0000	1.0000
SYMIG	42	-1389.6546	2863.3091	0.0000	1.0000
F81	38	-1399.8320	2875.6639	0.0000	1.0000
K2P	36	-1404.9205	2881.8409	0.0000	1.0000
SYM	40	-1402.9170	2885.8341	0.0000	1.0000
JC69G	36	-1412.4666	2896.9331	0.0000	1.0000
JC69I	36	-1413.0404	2898.0808	0.0000	1.0000
JC69IG	37	-1412.4017	2898.8034	0.0000	1.0000
JC69	35	-1425.4816	2920.9631	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1364.3672	2972.6574	0.6706	0.6706
HKYI	40	-1365.1891	2974.3012	0.2948	0.9654
HKYIG	41	-1364.2937	2978.6084	0.0342	0.9996
GTRG	44	-1360.0726	2988.4604	0.0002	0.9998
GTRI	44	-1361.0228	2990.3609	0.0001	0.9999
HKY	39	-1376.7922	2991.4093	0.0001	1.0000
GTRIG	45	-1360.0071	2994.4275	0.0000	1.0000
GTR	43	-1372.3360	3006.8892	0.0000	1.0000
K2PG	37	-1391.2836	3008.1960	0.0000	1.0000
K2PI	37	-1391.9283	3009.4854	0.0000	1.0000
F81G	39	-1387.1439	3012.1126	0.0000	1.0000
F81I	39	-1387.7950	3013.4149	0.0000	1.0000
K2PIG	38	-1391.1952	3014.1173	0.0000	1.0000
F81IG	40	-1387.0795	3018.0821	0.0000	1.0000
K2P	36	-1404.9205	3029.3716	0.0000	1.0000
SYMG	41	-1389.7378	3029.4967	0.0000	1.0000
SYMI	41	-1390.3992	3030.8194	0.0000	1.0000
F81	38	-1399.8320	3031.3908	0.0000	1.0000
SYMIG	42	-1389.6546	3035.4283	0.0000	1.0000
JC69G	36	-1412.4666	3044.4638	0.0000	1.0000
JC69I	36	-1413.0404	3045.6114	0.0000	1.0000
SYM	40	-1402.9170	3049.7570	0.0000	1.0000
JC69IG	37	-1412.4017	3050.4322	0.0000	1.0000
JC69	35	-1425.4816	3064.3957	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_3342.phylip = 1 - 445;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3342.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3342.phylip = 1 - 445;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3342.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/chr5_3342.phylip = 1 - 445;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_3342.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

