
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:13 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/chr4_10574.phylip" (19 taxa, 278 characters)

Minimum AIC  model: K2PG
Minimum AICc model: K2PG
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
K2PG	37	-742.5886	1570.8938	0.5230	0.5230
K2PI	37	-743.6746	1573.0658	0.1766	0.6996
HKYI	40	-740.0120	1573.8637	0.1185	0.8181
HKYG	40	-740.2010	1574.2416	0.0981	0.9161
K2PIG	38	-744.0151	1576.4318	0.0328	0.9489
HKYIG	41	-740.2007	1576.9947	0.0248	0.9737
SYMG	41	-740.8714	1578.3360	0.0127	0.9864
SYMI	41	-741.9806	1580.5545	0.0042	0.9905
GTRI	44	-737.8166	1580.6290	0.0040	0.9946
GTRG	44	-737.9470	1580.8898	0.0035	0.9981
GTRIG	45	-737.9468	1583.7384	0.0008	0.9989
SYMIG	42	-742.3226	1584.0154	0.0007	0.9997
K2P	36	-751.7117	1586.4773	0.0002	0.9999
HKY	39	-748.6971	1588.5035	0.0001	1.0000
SYM	40	-749.3664	1592.5724	0.0000	1.0000
GTR	43	-745.6371	1593.4452	0.0000	1.0000
JC69G	36	-760.4736	1604.0012	0.0000	1.0000
JC69I	36	-761.6111	1606.2762	0.0000	1.0000
F81I	39	-757.9446	1606.9984	0.0000	1.0000
F81G	39	-758.1339	1607.3771	0.0000	1.0000
JC69IG	37	-761.9675	1609.6517	0.0000	1.0000
F81IG	40	-758.1336	1610.1069	0.0000	1.0000
JC69	35	-769.3508	1619.1148	0.0000	1.0000
F81	38	-766.6810	1621.7637	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
K2PG	37	-742.5886	1559.1771	0.3121	0.3121
HKYI	40	-740.0120	1560.0241	0.2043	0.5164
HKYG	40	-740.2010	1560.4019	0.1692	0.6855
K2PI	37	-743.6746	1561.3492	0.1053	0.7909
HKYIG	41	-740.2007	1562.4015	0.0622	0.8531
GTRI	44	-737.8166	1563.6333	0.0336	0.8868
SYMG	41	-740.8714	1563.7428	0.0318	0.9186
GTRG	44	-737.9470	1563.8941	0.0295	0.9481
K2PIG	38	-744.0151	1564.0301	0.0276	0.9757
GTRIG	45	-737.9468	1565.8935	0.0109	0.9865
SYMI	41	-741.9806	1565.9613	0.0105	0.9970
SYMIG	42	-742.3226	1568.6452	0.0027	0.9998
HKY	39	-748.6971	1575.3942	0.0001	0.9999
K2P	36	-751.7117	1575.4234	0.0001	0.9999
GTR	43	-745.6371	1577.2743	0.0000	1.0000
SYM	40	-749.3664	1578.7327	0.0000	1.0000
JC69G	36	-760.4736	1592.9472	0.0000	1.0000
F81I	39	-757.9446	1593.8892	0.0000	1.0000
F81G	39	-758.1339	1594.2679	0.0000	1.0000
JC69I	36	-761.6111	1595.2222	0.0000	1.0000
F81IG	40	-758.1336	1596.2672	0.0000	1.0000
JC69IG	37	-761.9675	1597.9351	0.0000	1.0000
JC69	35	-769.3508	1608.7016	0.0000	1.0000
F81	38	-766.6810	1609.3620	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-742.5886	1693.3991	0.7357	0.7357
K2PI	37	-743.6746	1695.5712	0.2483	0.9841
K2PIG	38	-744.0151	1701.8797	0.0106	0.9947
HKYI	40	-740.0120	1705.1289	0.0021	0.9968
HKYG	40	-740.2010	1705.5068	0.0017	0.9985
K2P	36	-751.7117	1706.0178	0.0013	0.9998
HKYIG	41	-740.2007	1711.1339	0.0001	0.9999
SYMG	41	-740.8714	1712.4753	0.0001	1.0000
SYMI	41	-741.9806	1714.6937	0.0000	1.0000
HKY	39	-748.6971	1716.8715	0.0000	1.0000
SYMIG	42	-742.3226	1721.0053	0.0000	1.0000
GTRI	44	-737.8166	1723.2486	0.0000	1.0000
GTRG	44	-737.9470	1723.5094	0.0000	1.0000
JC69G	36	-760.4736	1723.5416	0.0000	1.0000
SYM	40	-749.3664	1723.8376	0.0000	1.0000
JC69I	36	-761.6111	1725.8166	0.0000	1.0000
GTRIG	45	-737.9468	1729.1365	0.0000	1.0000
JC69IG	37	-761.9675	1732.1570	0.0000	1.0000
GTR	43	-745.6371	1733.2620	0.0000	1.0000
F81I	39	-757.9446	1735.3664	0.0000	1.0000
JC69	35	-769.3508	1735.6684	0.0000	1.0000
F81G	39	-758.1339	1735.7451	0.0000	1.0000
F81IG	40	-758.1336	1741.3721	0.0000	1.0000
F81	38	-766.6810	1747.2116	0.0000	1.0000



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

[Mrbayes block for the best AIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10574.phylip = 1 - 278;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10574.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;


[Mrbayes block for the best AICc model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10574.phylip = 1 - 278;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10574.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;


[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/chr4_10574.phylip = 1 - 278;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10574.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

