
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:00 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/chr2_21320.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	-1113.0676	2315.6701	0.4330	0.4330
HKYI	40	-1113.2015	2315.9379	0.3787	0.8117
HKYIG	41	-1112.7619	2317.5646	0.1679	0.9796
GTRG	44	-1111.9666	2323.5802	0.0083	0.9879
GTRI	44	-1112.1337	2323.9145	0.0070	0.9949
GTRIG	45	-1111.6555	2325.5233	0.0031	0.9980
K2PG	37	-1123.0026	2328.1090	0.0009	0.9989
K2PI	37	-1123.3322	2328.7682	0.0006	0.9995
K2PIG	38	-1122.4206	2329.4077	0.0005	1.0000
SYMG	41	-1122.0987	2336.2383	0.0000	1.0000
SYMI	41	-1122.4915	2337.0238	0.0000	1.0000
SYMIG	42	-1121.4657	2337.4928	0.0000	1.0000
HKY	39	-1141.3615	2369.7665	0.0000	1.0000
GTR	43	-1140.5662	2378.2291	0.0000	1.0000
K2P	36	-1152.6857	2385.0265	0.0000	1.0000
SYM	40	-1151.6469	2392.8287	0.0000	1.0000
F81G	39	-1154.1737	2395.3909	0.0000	1.0000
F81I	39	-1154.2944	2395.6322	0.0000	1.0000
F81IG	40	-1154.0870	2397.7089	0.0000	1.0000
JC69G	36	-1163.2022	2406.0595	0.0000	1.0000
JC69I	36	-1163.3343	2406.3237	0.0000	1.0000
JC69IG	37	-1163.0015	2408.1067	0.0000	1.0000
F81	38	-1181.2168	2447.0001	0.0000	1.0000
JC69	35	-1190.3643	2457.9492	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1113.0676	2306.1353	0.3991	0.3991
HKYI	40	-1113.2015	2306.4030	0.3491	0.7481
HKYIG	41	-1112.7619	2307.5238	0.1993	0.9474
GTRG	44	-1111.9666	2311.9332	0.0220	0.9694
GTRI	44	-1112.1337	2312.2674	0.0186	0.9880
GTRIG	45	-1111.6555	2313.3109	0.0110	0.9990
K2PG	37	-1123.0026	2320.0053	0.0004	0.9994
K2PI	37	-1123.3322	2320.6645	0.0003	0.9997
K2PIG	38	-1122.4206	2320.8413	0.0003	1.0000
SYMG	41	-1122.0987	2326.1975	0.0000	1.0000
SYMIG	42	-1121.4657	2326.9314	0.0000	1.0000
SYMI	41	-1122.4915	2326.9830	0.0000	1.0000
HKY	39	-1141.3615	2360.7230	0.0000	1.0000
GTR	43	-1140.5662	2367.1323	0.0000	1.0000
K2P	36	-1152.6857	2377.3714	0.0000	1.0000
SYM	40	-1151.6469	2383.2938	0.0000	1.0000
F81G	39	-1154.1737	2386.3474	0.0000	1.0000
F81I	39	-1154.2944	2386.5887	0.0000	1.0000
F81IG	40	-1154.0870	2388.1740	0.0000	1.0000
JC69G	36	-1163.2022	2398.4044	0.0000	1.0000
JC69I	36	-1163.3343	2398.6685	0.0000	1.0000
JC69IG	37	-1163.0015	2400.0029	0.0000	1.0000
F81	38	-1181.2168	2438.4336	0.0000	1.0000
JC69	35	-1190.3643	2450.7285	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1113.0676	2464.2650	0.3837	0.3837
HKYI	40	-1113.2015	2464.5328	0.3356	0.7192
K2PG	37	-1123.0026	2466.2753	0.1404	0.8596
K2PI	37	-1123.3322	2466.9345	0.1010	0.9606
HKYIG	41	-1112.7619	2469.6068	0.0265	0.9872
K2PIG	38	-1122.4206	2471.0645	0.0128	1.0000
GTRG	44	-1111.9666	2485.8759	0.0000	1.0000
GTRI	44	-1112.1337	2486.2101	0.0000	1.0000
SYMG	41	-1122.0987	2488.2804	0.0000	1.0000
SYMI	41	-1122.4915	2489.0660	0.0000	1.0000
GTRIG	45	-1111.6555	2491.2069	0.0000	1.0000
SYMIG	42	-1121.4657	2492.9676	0.0000	1.0000
HKY	39	-1141.3615	2514.8995	0.0000	1.0000
K2P	36	-1152.6857	2519.6881	0.0000	1.0000
GTR	43	-1140.5662	2537.1218	0.0000	1.0000
F81G	39	-1154.1737	2540.5239	0.0000	1.0000
JC69G	36	-1163.2022	2540.7211	0.0000	1.0000
F81I	39	-1154.2944	2540.7652	0.0000	1.0000
JC69I	36	-1163.3343	2540.9853	0.0000	1.0000
SYM	40	-1151.6469	2541.4236	0.0000	1.0000
JC69IG	37	-1163.0015	2546.2729	0.0000	1.0000
F81IG	40	-1154.0870	2546.3037	0.0000	1.0000
F81	38	-1181.2168	2588.6569	0.0000	1.0000
JC69	35	-1190.3643	2589.0921	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/chr2_21320.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21320.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/chr2_21320.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21320.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/chr2_21320.phylip = 1 - 385;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21320.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

