
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:27 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_7244.phylip" (19 taxa, 661 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	-1384.7465	2854.7833	0.2443	0.2443
HKYI	40	-1384.7971	2854.8845	0.2323	0.4766
GTRG	44	-1380.5376	2855.5038	0.1704	0.6470
GTRI	44	-1380.6031	2855.6348	0.1596	0.8067
GTRIG	45	-1379.8545	2856.4406	0.1067	0.9133
HKYIG	41	-1384.6529	2856.8697	0.0861	0.9994
HKY	39	-1393.2899	2869.6039	0.0001	0.9996
K2PG	37	-1395.8310	2870.1756	0.0001	0.9997
K2PI	37	-1395.8630	2870.2396	0.0001	0.9998
GTR	43	-1389.2986	2870.7300	0.0001	0.9999
K2PIG	38	-1395.7548	2872.2749	0.0000	0.9999
SYMG	41	-1392.4338	2872.4315	0.0000	1.0000
SYMI	41	-1392.4833	2872.5305	0.0000	1.0000
SYMIG	42	-1392.3159	2874.4764	0.0000	1.0000
K2P	36	-1404.6746	2885.6184	0.0000	1.0000
SYM	40	-1401.2048	2887.6998	0.0000	1.0000
F81G	39	-1407.8598	2898.7437	0.0000	1.0000
F81I	39	-1407.9019	2898.8280	0.0000	1.0000
F81IG	40	-1407.7528	2900.7958	0.0000	1.0000
JC69G	36	-1418.2153	2912.6998	0.0000	1.0000
JC69I	36	-1418.2507	2912.7706	0.0000	1.0000
F81	38	-1416.6324	2914.0300	0.0000	1.0000
JC69IG	37	-1418.1110	2914.7356	0.0000	1.0000
JC69	35	-1427.1107	2928.2534	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1380.5376	2849.0752	0.2185	0.2185
GTRI	44	-1380.6031	2849.2062	0.2046	0.4231
HKYG	40	-1384.7465	2849.4930	0.1773	0.6003
HKYI	40	-1384.7971	2849.5942	0.1685	0.7689
GTRIG	45	-1379.8545	2849.7089	0.1591	0.9280
HKYIG	41	-1384.6529	2851.3059	0.0716	0.9996
HKY	39	-1393.2899	2864.5798	0.0001	0.9997
GTR	43	-1389.2986	2864.5971	0.0001	0.9998
K2PG	37	-1395.8310	2865.6620	0.0001	0.9999
K2PI	37	-1395.8630	2865.7260	0.0001	0.9999
SYMG	41	-1392.4338	2866.8677	0.0000	0.9999
SYMI	41	-1392.4833	2866.9667	0.0000	1.0000
K2PIG	38	-1395.7548	2867.5096	0.0000	1.0000
SYMIG	42	-1392.3159	2868.6317	0.0000	1.0000
K2P	36	-1404.6746	2881.3492	0.0000	1.0000
SYM	40	-1401.2048	2882.4095	0.0000	1.0000
F81G	39	-1407.8598	2893.7195	0.0000	1.0000
F81I	39	-1407.9019	2893.8039	0.0000	1.0000
F81IG	40	-1407.7528	2895.5055	0.0000	1.0000
JC69G	36	-1418.2153	2908.4305	0.0000	1.0000
JC69I	36	-1418.2507	2908.5014	0.0000	1.0000
F81	38	-1416.6324	2909.2648	0.0000	1.0000
JC69IG	37	-1418.1110	2910.2220	0.0000	1.0000
JC69	35	-1427.1107	2924.2214	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1384.7465	3029.2432	0.3962	0.3962
HKYI	40	-1384.7971	3029.3443	0.3766	0.7728
K2PG	37	-1395.8310	3031.9309	0.1033	0.8762
K2PI	37	-1395.8630	3031.9949	0.1001	0.9762
HKYIG	41	-1384.6529	3035.5498	0.0169	0.9932
K2PIG	38	-1395.7548	3038.2722	0.0043	0.9975
HKY	39	-1393.2899	3039.8362	0.0020	0.9995
K2P	36	-1404.6746	3043.1243	0.0004	0.9999
GTRG	44	-1380.5376	3046.8004	0.0001	0.9999
GTRI	44	-1380.6031	3046.9313	0.0001	1.0000
SYMG	41	-1392.4338	3051.1116	0.0000	1.0000
SYMI	41	-1392.4833	3051.2106	0.0000	1.0000
GTRIG	45	-1379.8545	3051.9279	0.0000	1.0000
SYMIG	42	-1392.3159	3057.3694	0.0000	1.0000
GTR	43	-1389.2986	3057.8286	0.0000	1.0000
SYM	40	-1401.2048	3062.1597	0.0000	1.0000
F81G	39	-1407.8598	3068.9759	0.0000	1.0000
F81I	39	-1407.9019	3069.0603	0.0000	1.0000
JC69G	36	-1418.2153	3070.2057	0.0000	1.0000
JC69I	36	-1418.2507	3070.2765	0.0000	1.0000
F81IG	40	-1407.7528	3075.2557	0.0000	1.0000
JC69IG	37	-1418.1110	3076.4909	0.0000	1.0000
F81	38	-1416.6324	3080.0274	0.0000	1.0000
JC69	35	-1427.1107	3081.5028	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/chr3_7244.phylip = 1 - 661;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7244.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/chr3_7244.phylip = 1 - 661;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7244.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/chr3_7244.phylip = 1 - 661;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7244.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

