
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:29 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/chr6_3231.phylip" (19 taxa, 385 characters)

Minimum AIC  model: HKYG
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	-1079.8542	2249.2433	0.5411	0.5411
HKYIG	41	-1079.4638	2250.9685	0.2284	0.7694
HKYI	40	-1080.8345	2251.2038	0.2030	0.9724
GTRG	44	-1078.3789	2256.4049	0.0151	0.9875
GTRIG	45	-1078.0333	2258.2790	0.0059	0.9934
GTRI	44	-1079.4097	2258.4665	0.0054	0.9988
K2PG	37	-1090.3058	2262.7154	0.0006	0.9994
K2PIG	38	-1089.8669	2264.3004	0.0003	0.9997
K2PI	37	-1091.1527	2264.4092	0.0003	1.0000
SYMG	41	-1090.0410	2272.1227	0.0000	1.0000
SYMI	41	-1090.8549	2273.7506	0.0000	1.0000
SYMIG	42	-1089.6301	2273.8216	0.0000	1.0000
HKY	39	-1095.6316	2278.3067	0.0000	1.0000
GTR	43	-1093.5961	2284.2890	0.0000	1.0000
K2P	36	-1107.0205	2293.6962	0.0000	1.0000
SYM	40	-1106.4744	2302.4836	0.0000	1.0000
F81G	39	-1110.3984	2307.8404	0.0000	1.0000
F81I	39	-1111.2849	2309.6133	0.0000	1.0000
F81IG	40	-1110.0565	2309.6479	0.0000	1.0000
JC69G	36	-1119.6956	2319.0465	0.0000	1.0000
JC69I	36	-1120.5426	2320.7404	0.0000	1.0000
JC69IG	37	-1119.3202	2320.7442	0.0000	1.0000
F81	38	-1125.8090	2336.1846	0.0000	1.0000
JC69	35	-1135.6693	2348.5593	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1079.8542	2239.7084	0.4830	0.4830
HKYIG	41	-1079.4638	2240.9277	0.2626	0.7456
HKYI	40	-1080.8345	2241.6689	0.1812	0.9268
GTRG	44	-1078.3789	2244.7579	0.0387	0.9655
GTRIG	45	-1078.0333	2246.0666	0.0201	0.9856
GTRI	44	-1079.4097	2246.8194	0.0138	0.9994
K2PG	37	-1090.3058	2254.6117	0.0003	0.9997
K2PIG	38	-1089.8669	2255.7339	0.0002	0.9999
K2PI	37	-1091.1527	2256.3054	0.0001	1.0000
SYMG	41	-1090.0410	2262.0819	0.0000	1.0000
SYMIG	42	-1089.6301	2263.2602	0.0000	1.0000
SYMI	41	-1090.8549	2263.7098	0.0000	1.0000
HKY	39	-1095.6316	2269.2632	0.0000	1.0000
GTR	43	-1093.5961	2273.1922	0.0000	1.0000
K2P	36	-1107.0205	2286.0410	0.0000	1.0000
SYM	40	-1106.4744	2292.9488	0.0000	1.0000
F81G	39	-1110.3984	2298.7969	0.0000	1.0000
F81IG	40	-1110.0565	2300.1130	0.0000	1.0000
F81I	39	-1111.2849	2300.5698	0.0000	1.0000
JC69G	36	-1119.6956	2311.3913	0.0000	1.0000
JC69IG	37	-1119.3202	2312.6404	0.0000	1.0000
JC69I	36	-1120.5426	2313.0852	0.0000	1.0000
F81	38	-1125.8090	2327.6181	0.0000	1.0000
JC69	35	-1135.6693	2341.3387	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1079.8542	2397.8382	0.5619	0.5619
HKYI	40	-1080.8345	2399.7986	0.2108	0.7727
K2PG	37	-1090.3058	2400.8817	0.1227	0.8954
K2PI	37	-1091.1527	2402.5754	0.0526	0.9480
HKYIG	41	-1079.4638	2403.0107	0.0423	0.9903
K2PIG	38	-1089.8669	2405.9571	0.0097	1.0000
GTRG	44	-1078.3789	2418.7006	0.0000	1.0000
GTRI	44	-1079.4097	2420.7621	0.0000	1.0000
HKY	39	-1095.6316	2423.4397	0.0000	1.0000
GTRIG	45	-1078.0333	2423.9625	0.0000	1.0000
SYMG	41	-1090.0410	2424.1649	0.0000	1.0000
SYMI	41	-1090.8549	2425.7928	0.0000	1.0000
K2P	36	-1107.0205	2428.3578	0.0000	1.0000
SYMIG	42	-1089.6301	2429.2964	0.0000	1.0000
GTR	43	-1093.5961	2443.1817	0.0000	1.0000
SYM	40	-1106.4744	2451.0785	0.0000	1.0000
F81G	39	-1110.3984	2452.9734	0.0000	1.0000
JC69G	36	-1119.6956	2453.7080	0.0000	1.0000
F81I	39	-1111.2849	2454.7463	0.0000	1.0000
JC69I	36	-1120.5426	2455.4020	0.0000	1.0000
F81IG	40	-1110.0565	2458.2428	0.0000	1.0000
JC69IG	37	-1119.3202	2458.9104	0.0000	1.0000
F81	38	-1125.8090	2477.8413	0.0000	1.0000
JC69	35	-1135.6693	2479.7022	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3231.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3231.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3231.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3231.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/chr6_3231.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3231.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

