
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:05 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/chr3_3177.phylip" (19 taxa, 385 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
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
GTRI	44	-1423.4380	2946.5231	0.5115	0.5115
GTRIG	45	-1422.7739	2947.7602	0.2756	0.7871
GTRG	44	-1424.3789	2948.4048	0.1996	0.9867
HKYG	40	-1432.6215	2954.7778	0.0082	0.9950
HKYIG	41	-1432.5113	2957.0634	0.0026	0.9976
HKYI	40	-1433.8678	2957.2704	0.0024	1.0000
F81G	39	-1448.1897	2983.4229	0.0000	1.0000
GTR	43	-1443.7117	2984.5201	0.0000	1.0000
F81IG	40	-1448.1300	2985.7949	0.0000	1.0000
F81I	39	-1450.5093	2988.0620	0.0000	1.0000
HKY	39	-1451.9695	2990.9824	0.0000	1.0000
F81	38	-1466.7610	3018.0884	0.0000	1.0000
K2PI	37	-1471.7846	3025.6730	0.0000	1.0000
K2PIG	38	-1471.6686	3027.9037	0.0000	1.0000
K2PG	37	-1474.9328	3031.9693	0.0000	1.0000
SYMG	41	-1471.9760	3035.9928	0.0000	1.0000
SYMI	41	-1472.5238	3037.0884	0.0000	1.0000
SYMIG	42	-1471.9682	3038.4978	0.0000	1.0000
K2P	36	-1492.4021	3064.4593	0.0000	1.0000
SYM	40	-1489.2546	3068.0442	0.0000	1.0000
JC69G	36	-1497.2185	3074.0922	0.0000	1.0000
JC69I	36	-1497.7021	3075.0594	0.0000	1.0000
JC69IG	37	-1497.1871	3076.4780	0.0000	1.0000
JC69	35	-1512.9977	3103.2160	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1423.4380	2934.8760	0.4729	0.4729
GTRIG	45	-1422.7739	2935.5478	0.3380	0.8109
GTRG	44	-1424.3789	2936.7577	0.1846	0.9955
HKYG	40	-1432.6215	2945.2430	0.0027	0.9981
HKYIG	41	-1432.5113	2947.0226	0.0011	0.9992
HKYI	40	-1433.8678	2947.7355	0.0008	1.0000
GTR	43	-1443.7117	2973.4234	0.0000	1.0000
F81G	39	-1448.1897	2974.3794	0.0000	1.0000
F81IG	40	-1448.1300	2976.2600	0.0000	1.0000
F81I	39	-1450.5093	2979.0185	0.0000	1.0000
HKY	39	-1451.9695	2981.9390	0.0000	1.0000
F81	38	-1466.7610	3009.5219	0.0000	1.0000
K2PI	37	-1471.7846	3017.5692	0.0000	1.0000
K2PIG	38	-1471.6686	3019.3373	0.0000	1.0000
K2PG	37	-1474.9328	3023.8655	0.0000	1.0000
SYMG	41	-1471.9760	3025.9520	0.0000	1.0000
SYMI	41	-1472.5238	3027.0476	0.0000	1.0000
SYMIG	42	-1471.9682	3027.9364	0.0000	1.0000
K2P	36	-1492.4021	3056.8041	0.0000	1.0000
SYM	40	-1489.2546	3058.5093	0.0000	1.0000
JC69G	36	-1497.2185	3066.4370	0.0000	1.0000
JC69I	36	-1497.7021	3067.4043	0.0000	1.0000
JC69IG	37	-1497.1871	3068.3742	0.0000	1.0000
JC69	35	-1512.9977	3095.9953	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1432.6215	3103.3727	0.6933	0.6933
HKYI	40	-1433.8678	3105.8653	0.1994	0.8927
GTRI	44	-1423.4380	3108.8187	0.0455	0.9383
HKYIG	41	-1432.5113	3109.1056	0.0395	0.9777
GTRG	44	-1424.3789	3110.7004	0.0178	0.9955
GTRIG	45	-1422.7739	3113.4438	0.0045	1.0000
F81G	39	-1448.1897	3128.5559	0.0000	1.0000
F81I	39	-1450.5093	3133.1950	0.0000	1.0000
F81IG	40	-1448.1300	3134.3897	0.0000	1.0000
HKY	39	-1451.9695	3136.1155	0.0000	1.0000
GTR	43	-1443.7117	3143.4128	0.0000	1.0000
F81	38	-1466.7610	3159.7452	0.0000	1.0000
K2PI	37	-1471.7846	3163.8392	0.0000	1.0000
K2PIG	38	-1471.6686	3169.5605	0.0000	1.0000
K2PG	37	-1474.9328	3170.1355	0.0000	1.0000
SYMG	41	-1471.9760	3188.0350	0.0000	1.0000
SYMI	41	-1472.5238	3189.1306	0.0000	1.0000
SYMIG	42	-1471.9682	3193.9726	0.0000	1.0000
K2P	36	-1492.4021	3199.1209	0.0000	1.0000
JC69G	36	-1497.2185	3208.7538	0.0000	1.0000
JC69I	36	-1497.7021	3209.7210	0.0000	1.0000
JC69IG	37	-1497.1871	3214.6442	0.0000	1.0000
SYM	40	-1489.2546	3216.6390	0.0000	1.0000
JC69	35	-1512.9977	3234.3588	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/chr3_3177.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3177.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/chr3_3177.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3177.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3177.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3177.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;


-------------------------------------------------------------
End of Output

