
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:10 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_9749.phylip" (19 taxa, 426 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1208.7110	2515.8156	0.4566	0.4566
GTRI	44	-1208.8417	2516.0770	0.4007	0.8573
GTRIG	45	-1208.7253	2518.3453	0.1289	0.9862
HKYG	40	-1217.2942	2523.1079	0.0119	0.9981
HKYI	40	-1219.8383	2528.1960	0.0009	0.9991
HKYIG	41	-1219.5328	2530.0343	0.0004	0.9994
GTR	43	-1217.0776	2530.0611	0.0004	0.9998
HKY	39	-1224.0151	2534.1131	0.0000	0.9998
K2PI	37	-1226.6283	2534.5041	0.0000	0.9999
K2PG	37	-1226.6849	2534.6173	0.0000	0.9999
SYMI	41	-1222.0509	2535.0705	0.0000	1.0000
SYMG	41	-1222.0814	2535.1315	0.0000	1.0000
K2PIG	38	-1226.7097	2537.0784	0.0000	1.0000
SYMIG	42	-1222.0864	2537.6036	0.0000	1.0000
K2P	36	-1233.2059	2545.2602	0.0000	1.0000
SYM	40	-1229.0439	2546.6073	0.0000	1.0000
F81I	39	-1234.0295	2554.1420	0.0000	1.0000
F81G	39	-1234.0684	2554.2196	0.0000	1.0000
F81IG	40	-1234.0860	2556.6914	0.0000	1.0000
JC69I	36	-1241.9471	2562.7426	0.0000	1.0000
JC69G	36	-1242.0232	2562.8947	0.0000	1.0000
F81	38	-1240.4484	2564.5557	0.0000	1.0000
JC69IG	37	-1242.0455	2565.3383	0.0000	1.0000
JC69	35	-1248.3299	2573.1213	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1208.7110	2505.4219	0.4440	0.4440
GTRI	44	-1208.8417	2505.6833	0.3896	0.8336
GTRIG	45	-1208.7253	2507.4505	0.1610	0.9946
HKYG	40	-1217.2942	2514.5885	0.0045	0.9991
HKYI	40	-1219.8383	2519.6765	0.0004	0.9995
GTR	43	-1217.0776	2520.1553	0.0003	0.9998
HKYIG	41	-1219.5328	2521.0656	0.0002	0.9999
HKY	39	-1224.0151	2526.0302	0.0000	0.9999
SYMI	41	-1222.0509	2526.1017	0.0000	1.0000
SYMG	41	-1222.0814	2526.1628	0.0000	1.0000
K2PI	37	-1226.6283	2527.2567	0.0000	1.0000
K2PG	37	-1226.6849	2527.3698	0.0000	1.0000
SYMIG	42	-1222.0864	2528.1728	0.0000	1.0000
K2PIG	38	-1226.7097	2529.4195	0.0000	1.0000
SYM	40	-1229.0439	2538.0878	0.0000	1.0000
K2P	36	-1233.2059	2538.4118	0.0000	1.0000
F81I	39	-1234.0295	2546.0591	0.0000	1.0000
F81G	39	-1234.0684	2546.1367	0.0000	1.0000
F81IG	40	-1234.0860	2548.1720	0.0000	1.0000
JC69I	36	-1241.9471	2555.8943	0.0000	1.0000
JC69G	36	-1242.0232	2556.0464	0.0000	1.0000
F81	38	-1240.4484	2556.8968	0.0000	1.0000
JC69IG	37	-1242.0455	2558.0909	0.0000	1.0000
JC69	35	-1248.3299	2566.6598	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1217.2942	2676.7660	0.3657	0.3657
K2PI	37	-1226.6283	2677.2710	0.2841	0.6498
K2PG	37	-1226.6849	2677.3841	0.2685	0.9183
HKYI	40	-1219.8383	2681.8541	0.0287	0.9471
K2PIG	38	-1226.7097	2683.4882	0.0127	0.9598
GTRG	44	-1208.7110	2683.8173	0.0108	0.9705
GTRI	44	-1208.8417	2684.0786	0.0094	0.9800
HKY	39	-1224.0151	2684.1533	0.0091	0.9891
K2P	36	-1233.2059	2684.3717	0.0082	0.9972
HKYIG	41	-1219.5328	2687.2976	0.0019	0.9991
GTRIG	45	-1208.7253	2689.9003	0.0005	0.9996
SYMI	41	-1222.0509	2692.3338	0.0002	0.9998
SYMG	41	-1222.0814	2692.3948	0.0001	0.9999
GTR	43	-1217.0776	2694.4962	0.0001	1.0000
SYMIG	42	-1222.0864	2698.4593	0.0000	1.0000
SYM	40	-1229.0439	2700.2654	0.0000	1.0000
JC69I	36	-1241.9471	2701.8541	0.0000	1.0000
JC69G	36	-1242.0232	2702.0062	0.0000	1.0000
F81I	39	-1234.0295	2704.1822	0.0000	1.0000
F81G	39	-1234.0684	2704.2598	0.0000	1.0000
JC69IG	37	-1242.0455	2708.1052	0.0000	1.0000
JC69	35	-1248.3299	2708.5652	0.0000	1.0000
F81IG	40	-1234.0860	2710.3495	0.0000	1.0000
F81	38	-1240.4484	2710.9655	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_9749.phylip = 1 - 426;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9749.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9749.phylip = 1 - 426;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9749.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 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_9749.phylip = 1 - 426;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9749.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

