
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:15 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_1378.phylip" (19 taxa, 312 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	-1126.9439	2356.7192	0.4286	0.4286
HKYG	40	-1133.0119	2358.1272	0.2120	0.6405
GTRI	44	-1128.2718	2359.3751	0.1136	0.7541
GTRIG	45	-1126.9450	2359.4540	0.1092	0.8633
HKYI	40	-1133.9893	2360.0820	0.0798	0.9431
HKYIG	41	-1133.0127	2360.7810	0.0562	0.9993
HKY	39	-1140.8985	2371.2676	0.0003	0.9996
K2PG	37	-1143.8148	2371.8923	0.0002	0.9998
GTR	43	-1136.1823	2372.4840	0.0002	1.0000
K2PI	37	-1146.4040	2377.0707	0.0000	1.0000
SYMG	41	-1142.1403	2379.0362	0.0000	1.0000
K2PIG	38	-1146.1211	2379.0994	0.0000	1.0000
K2P	36	-1150.8896	2383.4665	0.0000	1.0000
SYMI	41	-1144.7359	2384.2273	0.0000	1.0000
SYMIG	42	-1144.3607	2386.1488	0.0000	1.0000
SYM	40	-1149.2805	2390.6643	0.0000	1.0000
F81G	39	-1158.8767	2407.2241	0.0000	1.0000
F81I	39	-1159.2084	2407.8873	0.0000	1.0000
F81IG	40	-1158.8804	2409.8642	0.0000	1.0000
JC69G	36	-1165.8903	2413.4678	0.0000	1.0000
F81	38	-1163.7069	2414.2709	0.0000	1.0000
JC69I	36	-1168.4228	2418.5328	0.0000	1.0000
JC69IG	37	-1168.1870	2420.6367	0.0000	1.0000
JC69	35	-1172.6184	2424.3672	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1126.9439	2341.8877	0.5396	0.5396
GTRIG	45	-1126.9450	2343.8901	0.1983	0.7378
GTRI	44	-1128.2718	2344.5437	0.1430	0.8808
HKYG	40	-1133.0119	2346.0238	0.0682	0.9490
HKYI	40	-1133.9893	2347.9787	0.0257	0.9747
HKYIG	41	-1133.0127	2348.0254	0.0251	0.9998
GTR	43	-1136.1823	2358.3646	0.0001	0.9999
HKY	39	-1140.8985	2359.7970	0.0001	1.0000
K2PG	37	-1143.8148	2361.6295	0.0000	1.0000
SYMG	41	-1142.1403	2366.2806	0.0000	1.0000
K2PI	37	-1146.4040	2366.8080	0.0000	1.0000
K2PIG	38	-1146.1211	2368.2422	0.0000	1.0000
SYMI	41	-1144.7359	2371.4717	0.0000	1.0000
SYMIG	42	-1144.3607	2372.7213	0.0000	1.0000
K2P	36	-1150.8896	2373.7792	0.0000	1.0000
SYM	40	-1149.2805	2378.5610	0.0000	1.0000
F81G	39	-1158.8767	2395.7535	0.0000	1.0000
F81I	39	-1159.2084	2396.4167	0.0000	1.0000
F81IG	40	-1158.8804	2397.7609	0.0000	1.0000
F81	38	-1163.7069	2403.4138	0.0000	1.0000
JC69G	36	-1165.8903	2403.7805	0.0000	1.0000
JC69I	36	-1168.4228	2408.8455	0.0000	1.0000
JC69IG	37	-1168.1870	2410.3739	0.0000	1.0000
JC69	35	-1172.6184	2415.2367	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1133.0119	2495.7440	0.6377	0.6377
HKYI	40	-1133.9893	2497.6988	0.2399	0.8776
K2PG	37	-1143.8148	2500.1206	0.0715	0.9491
HKYIG	41	-1133.0127	2501.4886	0.0361	0.9852
K2PI	37	-1146.4040	2505.2991	0.0054	0.9905
HKY	39	-1140.8985	2505.7741	0.0042	0.9948
GTRG	44	-1126.9439	2506.5799	0.0028	0.9976
K2P	36	-1150.8896	2508.5273	0.0011	0.9987
GTRI	44	-1128.2718	2509.2358	0.0007	0.9994
K2PIG	38	-1146.1211	2510.4764	0.0004	0.9998
GTRIG	45	-1126.9450	2512.3252	0.0002	1.0000
GTR	43	-1136.1823	2519.3138	0.0000	1.0000
SYMG	41	-1142.1403	2519.7437	0.0000	1.0000
SYMI	41	-1144.7359	2524.9349	0.0000	1.0000
SYM	40	-1149.2805	2528.2811	0.0000	1.0000
SYMIG	42	-1144.3607	2529.9275	0.0000	1.0000
JC69G	36	-1165.8903	2538.5286	0.0000	1.0000
F81G	39	-1158.8767	2541.7306	0.0000	1.0000
F81I	39	-1159.2084	2542.3938	0.0000	1.0000
JC69I	36	-1168.4228	2543.5937	0.0000	1.0000
F81	38	-1163.7069	2545.6479	0.0000	1.0000
JC69	35	-1172.6184	2546.2419	0.0000	1.0000
F81IG	40	-1158.8804	2547.4810	0.0000	1.0000
JC69IG	37	-1168.1870	2548.8651	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_1378.phylip = 1 - 312;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_1378.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_1378.phylip = 1 - 312;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_1378.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_1378.phylip = 1 - 312;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_1378.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

