
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:10 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_5365.phylip" (19 taxa, 428 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1264.2327	2626.8049	0.4521	0.4521
GTRIG	45	-1263.5575	2627.9526	0.2547	0.7068
GTRI	44	-1265.3456	2629.0307	0.1486	0.8553
HKYG	40	-1271.1322	2630.7399	0.0632	0.9185
HKYIG	41	-1269.9701	2630.8625	0.0594	0.9780
HKYI	40	-1272.1859	2632.8472	0.0220	1.0000
K2PIG	38	-1287.8385	2659.2966	0.0000	1.0000
K2PG	37	-1289.4479	2660.1061	0.0000	1.0000
K2PI	37	-1290.3641	2661.9385	0.0000	1.0000
SYMIG	42	-1285.6555	2664.6929	0.0000	1.0000
SYMG	41	-1287.3870	2665.6963	0.0000	1.0000
SYMI	41	-1287.9186	2666.7595	0.0000	1.0000
GTR	43	-1297.1112	2690.0766	0.0000	1.0000
HKY	39	-1304.7119	2695.4650	0.0000	1.0000
F81G	39	-1308.7924	2703.6261	0.0000	1.0000
F81IG	40	-1307.6197	2703.7149	0.0000	1.0000
F81I	39	-1309.7338	2705.5088	0.0000	1.0000
JC69IG	37	-1322.7128	2726.6359	0.0000	1.0000
K2P	36	-1324.9886	2728.7905	0.0000	1.0000
JC69I	36	-1325.1104	2729.0340	0.0000	1.0000
JC69G	36	-1325.1169	2729.0470	0.0000	1.0000
SYM	40	-1321.4582	2731.3919	0.0000	1.0000
F81	38	-1342.5059	2768.6314	0.0000	1.0000
JC69	35	-1360.3938	2797.2162	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1264.2327	2616.4655	0.4565	0.4565
GTRIG	45	-1263.5575	2617.1149	0.3300	0.7865
GTRI	44	-1265.3456	2618.6913	0.1500	0.9365
HKYIG	41	-1269.9701	2621.9402	0.0296	0.9661
HKYG	40	-1271.1322	2622.2644	0.0251	0.9912
HKYI	40	-1272.1859	2624.3718	0.0088	1.0000
K2PIG	38	-1287.8385	2651.6770	0.0000	1.0000
K2PG	37	-1289.4479	2652.8958	0.0000	1.0000
K2PI	37	-1290.3641	2654.7282	0.0000	1.0000
SYMIG	42	-1285.6555	2655.3111	0.0000	1.0000
SYMG	41	-1287.3870	2656.7740	0.0000	1.0000
SYMI	41	-1287.9186	2657.8372	0.0000	1.0000
GTR	43	-1297.1112	2680.2224	0.0000	1.0000
HKY	39	-1304.7119	2687.4238	0.0000	1.0000
F81IG	40	-1307.6197	2695.2394	0.0000	1.0000
F81G	39	-1308.7924	2695.5849	0.0000	1.0000
F81I	39	-1309.7338	2697.4675	0.0000	1.0000
JC69IG	37	-1322.7128	2719.4257	0.0000	1.0000
K2P	36	-1324.9886	2721.9772	0.0000	1.0000
JC69I	36	-1325.1104	2722.2207	0.0000	1.0000
JC69G	36	-1325.1169	2722.2337	0.0000	1.0000
SYM	40	-1321.4582	2722.9164	0.0000	1.0000
F81	38	-1342.5059	2761.0118	0.0000	1.0000
JC69	35	-1360.3938	2790.7876	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1271.1322	2784.6294	0.6618	0.6618
HKYI	40	-1272.1859	2786.7367	0.2307	0.8925
HKYIG	41	-1269.9701	2788.3643	0.1023	0.9948
GTRG	44	-1264.2327	2795.0669	0.0036	0.9984
GTRI	44	-1265.3456	2797.2927	0.0012	0.9996
GTRIG	45	-1263.5575	2799.7754	0.0003	0.9999
K2PG	37	-1289.4479	2803.0834	0.0001	1.0000
K2PI	37	-1290.3641	2804.9158	0.0000	1.0000
K2PIG	38	-1287.8385	2805.9237	0.0000	1.0000
SYMG	41	-1287.3870	2823.1981	0.0000	1.0000
SYMI	41	-1287.9186	2824.2613	0.0000	1.0000
SYMIG	42	-1285.6555	2825.7942	0.0000	1.0000
HKY	39	-1304.7119	2845.7296	0.0000	1.0000
F81G	39	-1308.7924	2853.8907	0.0000	1.0000
GTR	43	-1297.1112	2854.7647	0.0000	1.0000
F81I	39	-1309.7338	2855.7733	0.0000	1.0000
F81IG	40	-1307.6197	2857.6044	0.0000	1.0000
K2P	36	-1324.9886	2868.1057	0.0000	1.0000
JC69I	36	-1325.1104	2868.3492	0.0000	1.0000
JC69G	36	-1325.1169	2868.3622	0.0000	1.0000
JC69IG	37	-1322.7128	2869.6132	0.0000	1.0000
SYM	40	-1321.4582	2885.2813	0.0000	1.0000
F81	38	-1342.5059	2915.2585	0.0000	1.0000
JC69	35	-1360.3938	2932.8570	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/chr1_5365.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5365.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/chr1_5365.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5365.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5365.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5365.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

