
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:36 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_17005.phylip" (19 taxa, 445 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-1255.7795	2611.9350	0.2873	0.2873
HKYIG	41	-1260.9867	2612.5193	0.2145	0.5017
HKYG	40	-1262.3254	2612.7696	0.1892	0.6910
GTRG	44	-1257.6543	2613.2085	0.1520	0.8429
HKYI	40	-1262.9979	2614.1146	0.0966	0.9395
GTRI	44	-1258.7422	2615.3844	0.0512	0.9907
K2PG	37	-1270.3404	2621.5898	0.0023	0.9930
K2PIG	38	-1269.2062	2621.7129	0.0022	0.9952
SYMIG	42	-1264.6338	2622.2526	0.0017	0.9968
SYMG	41	-1266.0739	2622.6938	0.0013	0.9981
K2PI	37	-1270.9220	2622.7532	0.0013	0.9994
SYMI	41	-1266.9156	2624.3772	0.0006	1.0000
F81G	39	-1277.0945	2639.8928	0.0000	1.0000
F81IG	40	-1275.9236	2639.9660	0.0000	1.0000
F81I	39	-1277.7333	2641.1704	0.0000	1.0000
JC69G	36	-1283.9773	2646.4840	0.0000	1.0000
JC69IG	37	-1282.8964	2646.7019	0.0000	1.0000
JC69I	36	-1284.5745	2647.6784	0.0000	1.0000
GTR	43	-1286.9640	2669.3643	0.0000	1.0000
HKY	39	-1291.8553	2669.4142	0.0000	1.0000
K2P	36	-1299.5508	2677.6311	0.0000	1.0000
SYM	40	-1294.8900	2677.8988	0.0000	1.0000
F81	38	-1305.8680	2695.0365	0.0000	1.0000
JC69	35	-1312.6647	2701.4907	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1255.7795	2601.5590	0.4571	0.4571
GTRG	44	-1257.6543	2603.3085	0.1906	0.6477
HKYIG	41	-1260.9867	2603.9734	0.1367	0.7844
HKYG	40	-1262.3254	2604.6508	0.0974	0.8818
GTRI	44	-1258.7422	2605.4844	0.0642	0.9460
HKYI	40	-1262.9979	2605.9958	0.0497	0.9957
SYMIG	42	-1264.6338	2613.2675	0.0013	0.9970
SYMG	41	-1266.0739	2614.1479	0.0008	0.9979
K2PIG	38	-1269.2062	2614.4124	0.0007	0.9986
K2PG	37	-1270.3404	2614.6807	0.0006	0.9993
SYMI	41	-1266.9156	2615.8313	0.0004	0.9996
K2PI	37	-1270.9220	2615.8441	0.0004	1.0000
F81IG	40	-1275.9236	2631.8472	0.0000	1.0000
F81G	39	-1277.0945	2632.1891	0.0000	1.0000
F81I	39	-1277.7333	2633.4667	0.0000	1.0000
JC69IG	37	-1282.8964	2639.7928	0.0000	1.0000
JC69G	36	-1283.9773	2639.9546	0.0000	1.0000
JC69I	36	-1284.5745	2641.1490	0.0000	1.0000
GTR	43	-1286.9640	2659.9279	0.0000	1.0000
HKY	39	-1291.8553	2661.7105	0.0000	1.0000
SYM	40	-1294.8900	2669.7800	0.0000	1.0000
K2P	36	-1299.5508	2671.1016	0.0000	1.0000
F81	38	-1305.8680	2687.7360	0.0000	1.0000
JC69	35	-1312.6647	2695.3294	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1270.3404	2766.3095	0.4440	0.4440
K2PI	37	-1270.9220	2767.4728	0.2482	0.6921
HKYG	40	-1262.3254	2768.5738	0.1431	0.8352
HKYI	40	-1262.9979	2769.9187	0.0730	0.9083
K2PIG	38	-1269.2062	2770.1393	0.0654	0.9737
HKYIG	41	-1260.9867	2771.9945	0.0259	0.9996
SYMG	41	-1266.0739	2782.1689	0.0002	0.9998
GTRG	44	-1257.6543	2783.6238	0.0001	0.9998
SYMI	41	-1266.9156	2783.8523	0.0001	0.9999
SYMIG	42	-1264.6338	2785.3866	0.0000	0.9999
GTRI	44	-1258.7422	2785.7996	0.0000	1.0000
GTRIG	45	-1255.7795	2785.9724	0.0000	1.0000
JC69G	36	-1283.9773	2787.4853	0.0000	1.0000
JC69I	36	-1284.5745	2788.6796	0.0000	1.0000
JC69IG	37	-1282.8964	2791.4215	0.0000	1.0000
F81G	39	-1277.0945	2792.0140	0.0000	1.0000
F81I	39	-1277.7333	2793.2916	0.0000	1.0000
F81IG	40	-1275.9236	2795.7702	0.0000	1.0000
K2P	36	-1299.5508	2818.6323	0.0000	1.0000
HKY	39	-1291.8553	2821.5354	0.0000	1.0000
SYM	40	-1294.8900	2833.7030	0.0000	1.0000
GTR	43	-1286.9640	2836.1451	0.0000	1.0000
JC69	35	-1312.6647	2838.7620	0.0000	1.0000
F81	38	-1305.8680	2843.4628	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/chr2_17005.phylip = 1 - 445;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17005.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/chr2_17005.phylip = 1 - 445;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17005.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17005.phylip = 1 - 445;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_17005.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

