
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:15 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_5062.phylip" (19 taxa, 417 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-1341.3799	2781.4049	0.5136	0.5136
GTRG	44	-1341.9771	2782.5994	0.2826	0.7962
GTRIG	45	-1341.3882	2783.9354	0.1449	0.9411
HKYI	40	-1349.0838	2786.8910	0.0331	0.9742
HKYG	40	-1349.7937	2788.3108	0.0163	0.9904
HKYIG	41	-1349.0962	2789.3763	0.0095	1.0000
GTR	43	-1352.2033	2800.5514	0.0000	1.0000
HKY	39	-1360.1267	2806.5293	0.0000	1.0000
K2PI	37	-1365.4349	2812.2893	0.0000	1.0000
K2PG	37	-1366.0516	2813.5227	0.0000	1.0000
K2PIG	38	-1365.4436	2814.7285	0.0000	1.0000
SYMI	41	-1361.9398	2815.0635	0.0000	1.0000
SYMG	41	-1362.8125	2816.8089	0.0000	1.0000
SYMIG	42	-1361.9548	2817.5674	0.0000	1.0000
K2P	36	-1377.2033	2833.4172	0.0000	1.0000
SYM	40	-1373.1335	2834.9904	0.0000	1.0000
F81I	39	-1374.8531	2835.9820	0.0000	1.0000
F81G	39	-1375.1103	2836.4965	0.0000	1.0000
F81IG	40	-1374.8572	2838.4378	0.0000	1.0000
F81	38	-1384.3645	2852.5702	0.0000	1.0000
JC69I	36	-1388.2837	2855.5780	0.0000	1.0000
JC69G	36	-1388.4962	2856.0029	0.0000	1.0000
JC69IG	37	-1388.4852	2858.3900	0.0000	1.0000
JC69	35	-1398.1773	2872.9688	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1341.3799	2770.7597	0.5100	0.5100
GTRG	44	-1341.9771	2771.9542	0.2806	0.7906
GTRIG	45	-1341.3882	2772.7764	0.1861	0.9767
HKYI	40	-1349.0838	2778.1676	0.0126	0.9892
HKYG	40	-1349.7937	2779.5874	0.0062	0.9954
HKYIG	41	-1349.0962	2780.1923	0.0046	1.0000
GTR	43	-1352.2033	2790.4066	0.0000	1.0000
HKY	39	-1360.1267	2798.2534	0.0000	1.0000
K2PI	37	-1365.4349	2804.8698	0.0000	1.0000
SYMI	41	-1361.9398	2805.8795	0.0000	1.0000
K2PG	37	-1366.0516	2806.1032	0.0000	1.0000
K2PIG	38	-1365.4436	2806.8872	0.0000	1.0000
SYMG	41	-1362.8125	2807.6249	0.0000	1.0000
SYMIG	42	-1361.9548	2807.9096	0.0000	1.0000
SYM	40	-1373.1335	2826.2670	0.0000	1.0000
K2P	36	-1377.2033	2826.4067	0.0000	1.0000
F81I	39	-1374.8531	2827.7061	0.0000	1.0000
F81G	39	-1375.1103	2828.2207	0.0000	1.0000
F81IG	40	-1374.8572	2829.7144	0.0000	1.0000
F81	38	-1384.3645	2844.7289	0.0000	1.0000
JC69I	36	-1388.2837	2848.5674	0.0000	1.0000
JC69G	36	-1388.4962	2848.9924	0.0000	1.0000
JC69IG	37	-1388.4852	2850.9705	0.0000	1.0000
JC69	35	-1398.1773	2866.3546	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1349.0838	2939.4911	0.6403	0.6403
HKYG	40	-1349.7937	2940.9108	0.3148	0.9551
HKYIG	41	-1349.0962	2945.5489	0.0310	0.9860
GTRI	44	-1341.3799	2948.2155	0.0082	0.9942
GTRG	44	-1341.9771	2949.4100	0.0045	0.9987
K2PI	37	-1365.4349	2954.0940	0.0004	0.9991
GTRIG	45	-1341.3882	2954.2652	0.0004	0.9995
K2PG	37	-1366.0516	2955.3274	0.0002	0.9998
HKY	39	-1360.1267	2955.5438	0.0002	1.0000
K2PIG	38	-1365.4436	2960.1445	0.0000	1.0000
GTR	43	-1352.2033	2963.8293	0.0000	1.0000
SYMI	41	-1361.9398	2971.2361	0.0000	1.0000
K2P	36	-1377.2033	2971.5978	0.0000	1.0000
SYMG	41	-1362.8125	2972.9815	0.0000	1.0000
SYMIG	42	-1361.9548	2977.2992	0.0000	1.0000
F81I	39	-1374.8531	2984.9965	0.0000	1.0000
F81G	39	-1375.1103	2985.5110	0.0000	1.0000
SYM	40	-1373.1335	2987.5904	0.0000	1.0000
F81IG	40	-1374.8572	2991.0379	0.0000	1.0000
JC69I	36	-1388.2837	2993.7585	0.0000	1.0000
JC69G	36	-1388.4962	2994.1835	0.0000	1.0000
F81	38	-1384.3645	2997.9862	0.0000	1.0000
JC69IG	37	-1388.4852	3000.1947	0.0000	1.0000
JC69	35	-1398.1773	3007.5126	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_5062.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_5062.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_5062.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_5062.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_5062.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_5062.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;


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End of Output

