
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:05 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_14247.phylip" (19 taxa, 262 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1137.0321	2380.3130	0.5560	0.5560
GTRIG	45	-1136.6108	2382.3883	0.1970	0.7530
SYMG	41	-1143.2790	2384.2126	0.0791	0.8322
HKYG	40	-1144.9315	2384.7046	0.0619	0.8940
K2PG	37	-1149.6004	2385.7544	0.0366	0.9306
SYMIG	42	-1142.7965	2386.0861	0.0310	0.9616
HKYIG	41	-1144.5932	2386.8410	0.0213	0.9829
K2PIG	38	-1149.1832	2387.6578	0.0141	0.9970
GTRI	44	-1143.4093	2393.0674	0.0009	0.9980
SYMI	41	-1147.8493	2393.3531	0.0008	0.9988
K2PI	37	-1153.6446	2393.8429	0.0006	0.9994
HKYI	40	-1149.6275	2394.0967	0.0006	1.0000
GTR	43	-1163.4992	2430.3561	0.0000	1.0000
HKY	39	-1169.5557	2431.1655	0.0000	1.0000
SYM	40	-1168.4975	2431.8366	0.0000	1.0000
K2P	36	-1174.0763	2431.9925	0.0000	1.0000
JC69G	36	-1175.6964	2435.2328	0.0000	1.0000
F81G	39	-1171.8253	2435.7047	0.0000	1.0000
JC69IG	37	-1175.2943	2437.1421	0.0000	1.0000
F81IG	40	-1171.4395	2437.7207	0.0000	1.0000
JC69I	36	-1179.5546	2442.9492	0.0000	1.0000
F81I	39	-1175.7732	2443.6004	0.0000	1.0000
JC69	35	-1199.1137	2479.3779	0.0000	1.0000
F81	38	-1195.4748	2480.2411	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1137.0321	2362.0641	0.6018	0.6018
GTRIG	45	-1136.6108	2363.2216	0.3374	0.9392
SYMG	41	-1143.2790	2368.5580	0.0234	0.9626
SYMIG	42	-1142.7965	2369.5930	0.0140	0.9765
HKYG	40	-1144.9315	2369.8629	0.0122	0.9887
HKYIG	41	-1144.5932	2371.1864	0.0063	0.9950
K2PG	37	-1149.6004	2373.2008	0.0023	0.9973
K2PIG	38	-1149.1832	2374.3663	0.0013	0.9986
GTRI	44	-1143.4093	2374.8186	0.0010	0.9996
SYMI	41	-1147.8493	2377.6986	0.0002	0.9998
HKYI	40	-1149.6275	2379.2551	0.0001	1.0000
K2PI	37	-1153.6446	2381.2893	0.0000	1.0000
GTR	43	-1163.4992	2412.9983	0.0000	1.0000
SYM	40	-1168.4975	2416.9950	0.0000	1.0000
HKY	39	-1169.5557	2417.1115	0.0000	1.0000
K2P	36	-1174.0763	2420.1525	0.0000	1.0000
F81G	39	-1171.8253	2421.6507	0.0000	1.0000
F81IG	40	-1171.4395	2422.8790	0.0000	1.0000
JC69G	36	-1175.6964	2423.3928	0.0000	1.0000
JC69IG	37	-1175.2943	2424.5886	0.0000	1.0000
F81I	39	-1175.7732	2429.5464	0.0000	1.0000
JC69I	36	-1179.5546	2431.1092	0.0000	1.0000
F81	38	-1195.4748	2466.9496	0.0000	1.0000
JC69	35	-1199.1137	2468.2275	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1149.6004	2505.2295	0.8704	0.8704
K2PIG	38	-1149.1832	2509.9634	0.0816	0.9520
HKYG	40	-1144.9315	2512.5967	0.0219	0.9739
K2PI	37	-1153.6446	2513.3180	0.0153	0.9891
SYMG	41	-1143.2790	2514.8602	0.0071	0.9962
HKYIG	41	-1144.5932	2517.4886	0.0019	0.9981
GTRG	44	-1137.0321	2519.0713	0.0009	0.9989
SYMIG	42	-1142.7965	2519.4634	0.0007	0.9996
HKYI	40	-1149.6275	2521.9889	0.0002	0.9998
GTRIG	45	-1136.6108	2523.7971	0.0001	0.9999
SYMI	41	-1147.8493	2524.0007	0.0001	1.0000
GTRI	44	-1143.4093	2531.8257	0.0000	1.0000
K2P	36	-1174.0763	2548.6129	0.0000	1.0000
JC69G	36	-1175.6964	2551.8532	0.0000	1.0000
HKY	39	-1169.5557	2556.2769	0.0000	1.0000
JC69IG	37	-1175.2943	2556.6173	0.0000	1.0000
JC69I	36	-1179.5546	2559.5696	0.0000	1.0000
SYM	40	-1168.4975	2559.7287	0.0000	1.0000
F81G	39	-1171.8253	2560.8161	0.0000	1.0000
F81IG	40	-1171.4395	2565.6128	0.0000	1.0000
GTR	43	-1163.4992	2566.4372	0.0000	1.0000
F81I	39	-1175.7732	2568.7118	0.0000	1.0000
JC69	35	-1199.1137	2593.1195	0.0000	1.0000
F81	38	-1195.4748	2602.5467	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/chr2_14247.phylip = 1 - 262;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14247.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/chr2_14247.phylip = 1 - 262;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14247.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14247.phylip = 1 - 262;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_14247.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

