
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:19 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/chr4_13431.phylip" (19 taxa, 361 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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	-1111.8390	2313.9280	0.1975	0.1975
GTRG	44	-1106.7936	2314.1188	0.1796	0.3771
HKYI	40	-1112.0882	2314.4263	0.1540	0.5310
GTRI	44	-1106.9714	2314.4745	0.1503	0.6813
K2PG	37	-1116.4716	2315.6490	0.0835	0.7649
K2PI	37	-1116.7683	2316.2426	0.0621	0.8270
HKYIG	41	-1111.7240	2316.2442	0.0620	0.8890
GTRIG	45	-1106.6677	2316.4783	0.0552	0.9442
K2PIG	38	-1116.3436	2317.8922	0.0272	0.9714
SYMG	41	-1112.9471	2318.6904	0.0183	0.9897
SYMI	41	-1113.8386	2320.4734	0.0075	0.9972
SYMIG	42	-1113.5355	2322.4295	0.0028	1.0000
HKY	39	-1123.0019	2333.7234	0.0000	1.0000
GTR	43	-1118.4411	2334.8190	0.0000	1.0000
K2P	36	-1127.6341	2335.4903	0.0000	1.0000
SYM	40	-1124.3727	2338.9954	0.0000	1.0000
JC69G	36	-1137.5850	2355.3921	0.0000	1.0000
F81G	39	-1133.9309	2355.5815	0.0000	1.0000
JC69I	36	-1138.8625	2357.9473	0.0000	1.0000
F81I	39	-1135.1817	2358.0831	0.0000	1.0000
JC69IG	37	-1138.4854	2359.6768	0.0000	1.0000
F81IG	40	-1134.8282	2359.9064	0.0000	1.0000
JC69	35	-1147.8098	2373.3734	0.0000	1.0000
F81	38	-1144.1093	2373.4236	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1106.7936	2301.5872	0.3084	0.3084
GTRI	44	-1106.9714	2301.9429	0.2582	0.5666
GTRIG	45	-1106.6677	2303.3355	0.1287	0.6953
HKYG	40	-1111.8390	2303.6780	0.1084	0.8037
HKYI	40	-1112.0882	2304.1763	0.0845	0.8882
HKYIG	41	-1111.7240	2305.4479	0.0447	0.9329
K2PG	37	-1116.4716	2306.9432	0.0212	0.9541
K2PI	37	-1116.7683	2307.5367	0.0157	0.9699
SYMG	41	-1112.9471	2307.8942	0.0132	0.9830
K2PIG	38	-1116.3436	2308.6873	0.0089	0.9919
SYMI	41	-1113.8386	2309.6772	0.0054	0.9973
SYMIG	42	-1113.5355	2311.0710	0.0027	1.0000
GTR	43	-1118.4411	2322.8821	0.0000	1.0000
HKY	39	-1123.0019	2324.0037	0.0000	1.0000
K2P	36	-1127.6341	2327.2681	0.0000	1.0000
SYM	40	-1124.3727	2328.7454	0.0000	1.0000
F81G	39	-1133.9309	2345.8619	0.0000	1.0000
JC69G	36	-1137.5850	2347.1699	0.0000	1.0000
F81I	39	-1135.1817	2348.3635	0.0000	1.0000
F81IG	40	-1134.8282	2349.6564	0.0000	1.0000
JC69I	36	-1138.8625	2349.7250	0.0000	1.0000
JC69IG	37	-1138.4854	2350.9709	0.0000	1.0000
F81	38	-1144.1093	2364.2186	0.0000	1.0000
JC69	35	-1147.8098	2365.6196	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1116.4716	2450.8316	0.5461	0.5461
K2PI	37	-1116.7683	2451.4252	0.4059	0.9519
K2PIG	38	-1116.3436	2456.4646	0.0327	0.9846
HKYG	40	-1111.8390	2459.2331	0.0082	0.9928
HKYI	40	-1112.0882	2459.7315	0.0064	0.9991
HKYIG	41	-1111.7240	2464.8919	0.0005	0.9996
K2P	36	-1127.6341	2467.2677	0.0001	0.9998
SYMG	41	-1112.9471	2467.3382	0.0001	0.9999
SYMI	41	-1113.8386	2469.1212	0.0001	1.0000
GTRG	44	-1106.7936	2472.6978	0.0000	1.0000
GTRI	44	-1106.9714	2473.0535	0.0000	1.0000
SYMIG	42	-1113.5355	2474.4039	0.0000	1.0000
HKY	39	-1123.0019	2475.6700	0.0000	1.0000
GTRIG	45	-1106.6677	2478.3350	0.0000	1.0000
SYM	40	-1124.3727	2484.3006	0.0000	1.0000
JC69G	36	-1137.5850	2487.1695	0.0000	1.0000
JC69I	36	-1138.8625	2489.7246	0.0000	1.0000
GTR	43	-1118.4411	2490.1039	0.0000	1.0000
JC69IG	37	-1138.4854	2494.8594	0.0000	1.0000
F81G	39	-1133.9309	2497.5281	0.0000	1.0000
F81I	39	-1135.1817	2500.0297	0.0000	1.0000
JC69	35	-1147.8098	2501.7303	0.0000	1.0000
F81IG	40	-1134.8282	2505.2116	0.0000	1.0000
F81	38	-1144.1093	2511.9960	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/chr4_13431.phylip = 1 - 361;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13431.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/chr4_13431.phylip = 1 - 361;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13431.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13431.phylip = 1 - 361;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13431.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

