
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:26 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/chr6_3198.phylip" (19 taxa, 217 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-577.7664	1254.1693	0.5115	0.5115
HKYI	40	-578.3060	1255.2483	0.2982	0.8098
HKYIG	41	-577.6744	1257.0288	0.1224	0.9322
HKY	39	-582.0012	1259.6296	0.0334	0.9656
GTRG	44	-575.0303	1261.0838	0.0161	0.9817
GTRI	44	-575.4389	1261.9010	0.0107	0.9924
GTRIG	45	-574.9064	1264.0233	0.0037	0.9961
K2PG	37	-588.0369	1265.7833	0.0015	0.9977
K2PI	37	-588.5637	1266.8370	0.0009	0.9986
GTR	43	-579.7218	1267.3164	0.0007	0.9993
K2PIG	38	-587.9351	1268.5219	0.0004	0.9997
K2P	36	-591.8194	1270.4387	0.0001	0.9998
SYMG	41	-585.1427	1271.9654	0.0001	0.9999
SYMI	41	-585.2180	1272.1160	0.0001	1.0000
SYMIG	42	-585.0160	1274.7907	0.0000	1.0000
SYM	40	-589.1205	1276.8774	0.0000	1.0000
F81G	39	-599.2641	1294.1554	0.0000	1.0000
F81I	39	-599.7569	1295.1409	0.0000	1.0000
F81IG	40	-599.2113	1297.0589	0.0000	1.0000
F81	38	-602.8803	1298.4123	0.0000	1.0000
JC69G	36	-607.5402	1301.8804	0.0000	1.0000
JC69I	36	-608.0254	1302.8509	0.0000	1.0000
JC69IG	37	-607.4804	1304.6702	0.0000	1.0000
JC69	35	-611.0435	1306.0096	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-577.7664	1235.5329	0.3813	0.3813
HKYI	40	-578.3060	1236.6119	0.2223	0.6036
HKYIG	41	-577.6744	1237.3488	0.1538	0.7574
GTRG	44	-575.0303	1238.0606	0.1077	0.8651
GTRI	44	-575.4389	1238.8778	0.0716	0.9367
GTRIG	45	-574.9064	1239.8128	0.0449	0.9815
HKY	39	-582.0012	1242.0024	0.0150	0.9966
GTR	43	-579.7218	1245.4435	0.0027	0.9992
K2PG	37	-588.0369	1250.0738	0.0003	0.9995
K2PI	37	-588.5637	1251.1275	0.0002	0.9997
K2PIG	38	-587.9351	1251.8702	0.0001	0.9998
SYMG	41	-585.1427	1252.2854	0.0001	0.9999
SYMI	41	-585.2180	1252.4360	0.0001	0.9999
SYMIG	42	-585.0160	1254.0320	0.0000	1.0000
K2P	36	-591.8194	1255.6387	0.0000	1.0000
SYM	40	-589.1205	1258.2411	0.0000	1.0000
F81G	39	-599.2641	1276.5283	0.0000	1.0000
F81I	39	-599.7569	1277.5138	0.0000	1.0000
F81IG	40	-599.2113	1278.4225	0.0000	1.0000
F81	38	-602.8803	1281.7606	0.0000	1.0000
JC69G	36	-607.5402	1287.0804	0.0000	1.0000
JC69I	36	-608.0254	1288.0509	0.0000	1.0000
JC69IG	37	-607.4804	1288.9607	0.0000	1.0000
JC69	35	-611.0435	1292.0870	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-577.7664	1370.7288	0.4778	0.4778
HKYI	40	-578.3060	1371.8078	0.2785	0.7563
HKY	39	-582.0012	1373.8184	0.1019	0.8582
K2PG	37	-588.0369	1375.1300	0.0529	0.9111
HKYIG	41	-577.6744	1375.9246	0.0356	0.9467
K2PI	37	-588.5637	1376.1837	0.0312	0.9779
K2P	36	-591.8194	1377.3150	0.0177	0.9957
K2PIG	38	-587.9351	1380.3063	0.0040	0.9997
GTRG	44	-575.0303	1386.7760	0.0002	0.9998
GTRI	44	-575.4389	1387.5932	0.0001	0.9999
GTR	43	-579.7218	1390.7791	0.0000	0.9999
SYMG	41	-585.1427	1390.8612	0.0000	1.0000
SYMI	41	-585.2180	1391.0118	0.0000	1.0000
GTRIG	45	-574.9064	1391.9082	0.0000	1.0000
SYM	40	-589.1205	1393.4370	0.0000	1.0000
SYMIG	42	-585.0160	1395.9877	0.0000	1.0000
F81G	39	-599.2641	1408.3443	0.0000	1.0000
JC69G	36	-607.5402	1408.7567	0.0000	1.0000
F81I	39	-599.7569	1409.3298	0.0000	1.0000
JC69I	36	-608.0254	1409.7272	0.0000	1.0000
F81	38	-602.8803	1410.1967	0.0000	1.0000
JC69	35	-611.0435	1410.3834	0.0000	1.0000
F81IG	40	-599.2113	1413.6184	0.0000	1.0000
JC69IG	37	-607.4804	1414.0169	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3198.phylip = 1 - 217;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3198.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3198.phylip = 1 - 217;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3198.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;


[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/chr6_3198.phylip = 1 - 217;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3198.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

