
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:01 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/chr1_25675.phylip" (19 taxa, 505 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYI


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
GTRIG	45	-1095.7091	2290.4379	0.3489	0.3489
HKYIG	41	-1100.7732	2290.9848	0.2654	0.6144
GTRI	44	-1097.2693	2291.1473	0.2447	0.8591
HKYI	40	-1102.6972	2292.4634	0.1267	0.9858
GTRG	44	-1100.7210	2298.0508	0.0078	0.9936
HKYG	40	-1105.7065	2298.4820	0.0063	0.9998
K2PIG	38	-1112.2031	2306.7666	0.0001	0.9999
K2PI	37	-1114.4786	2308.9786	0.0000	1.0000
SYMIG	42	-1108.8561	2309.5303	0.0000	1.0000
SYMI	41	-1110.8713	2311.1811	0.0000	1.0000
K2PG	37	-1117.8402	2315.7018	0.0000	1.0000
SYMG	41	-1113.8215	2317.0814	0.0000	1.0000
F81IG	40	-1116.5537	2320.1764	0.0000	1.0000
F81I	39	-1118.4791	2321.6679	0.0000	1.0000
F81G	39	-1122.0849	2328.8796	0.0000	1.0000
JC69IG	37	-1127.5332	2335.0879	0.0000	1.0000
JC69I	36	-1129.6412	2336.9747	0.0000	1.0000
JC69G	36	-1132.6889	2343.0701	0.0000	1.0000
HKY	39	-1129.3199	2343.3494	0.0000	1.0000
GTR	43	-1125.3266	2344.8615	0.0000	1.0000
K2P	36	-1142.4121	2362.5165	0.0000	1.0000
SYM	40	-1138.6324	2364.3337	0.0000	1.0000
F81	38	-1144.6918	2371.7441	0.0000	1.0000
JC69	35	-1155.5643	2386.5018	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1095.7091	2281.4183	0.4812	0.4812
GTRI	44	-1097.2693	2282.5386	0.2748	0.7560
HKYIG	41	-1100.7732	2283.5464	0.1660	0.9221
HKYI	40	-1102.6972	2285.3945	0.0659	0.9880
GTRG	44	-1100.7210	2289.4421	0.0087	0.9967
HKYG	40	-1105.7065	2291.4130	0.0033	0.9999
K2PIG	38	-1112.2031	2300.4061	0.0000	1.0000
SYMIG	42	-1108.8561	2301.7121	0.0000	1.0000
K2PI	37	-1114.4786	2302.9571	0.0000	1.0000
SYMI	41	-1110.8713	2303.7426	0.0000	1.0000
SYMG	41	-1113.8215	2309.6429	0.0000	1.0000
K2PG	37	-1117.8402	2309.6804	0.0000	1.0000
F81IG	40	-1116.5537	2313.1075	0.0000	1.0000
F81I	39	-1118.4791	2314.9582	0.0000	1.0000
F81G	39	-1122.0849	2322.1699	0.0000	1.0000
JC69IG	37	-1127.5332	2329.0665	0.0000	1.0000
JC69I	36	-1129.6412	2331.2824	0.0000	1.0000
HKY	39	-1129.3199	2336.6397	0.0000	1.0000
GTR	43	-1125.3266	2336.6533	0.0000	1.0000
JC69G	36	-1132.6889	2337.3778	0.0000	1.0000
K2P	36	-1142.4121	2356.8242	0.0000	1.0000
SYM	40	-1138.6324	2357.2647	0.0000	1.0000
F81	38	-1144.6918	2365.3836	0.0000	1.0000
JC69	35	-1155.5643	2381.1287	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1102.6972	2454.3768	0.6745	0.6745
HKYIG	41	-1100.7732	2456.7533	0.2056	0.8801
K2PI	37	-1114.4786	2459.2658	0.0585	0.9386
HKYG	40	-1105.7065	2460.3954	0.0333	0.9719
K2PIG	38	-1112.2031	2460.9393	0.0253	0.9972
K2PG	37	-1117.8402	2465.9891	0.0020	0.9992
GTRI	44	-1097.2693	2468.4192	0.0006	0.9998
GTRIG	45	-1095.7091	2471.5234	0.0001	1.0000
GTRG	44	-1100.7210	2475.3226	0.0000	1.0000
SYMI	41	-1110.8713	2476.9495	0.0000	1.0000
SYMIG	42	-1108.8561	2479.1436	0.0000	1.0000
F81I	39	-1118.4791	2479.7160	0.0000	1.0000
F81IG	40	-1116.5537	2482.0898	0.0000	1.0000
SYMG	41	-1113.8215	2482.8498	0.0000	1.0000
JC69I	36	-1129.6412	2483.3665	0.0000	1.0000
JC69IG	37	-1127.5332	2485.3751	0.0000	1.0000
F81G	39	-1122.0849	2486.9277	0.0000	1.0000
JC69G	36	-1132.6889	2489.4619	0.0000	1.0000
HKY	39	-1129.3199	2501.3975	0.0000	1.0000
K2P	36	-1142.4121	2508.9083	0.0000	1.0000
GTR	43	-1125.3266	2518.3093	0.0000	1.0000
F81	38	-1144.6918	2525.9168	0.0000	1.0000
SYM	40	-1138.6324	2526.2470	0.0000	1.0000
JC69	35	-1155.5643	2528.9882	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25675.phylip = 1 - 505;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25675.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25675.phylip = 1 - 505;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25675.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25675.phylip = 1 - 505;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25675.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

