
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:44 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_11187.phylip" (19 taxa, 258 characters)

Minimum AIC  model: GTRG
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	-749.1139	1593.3430	0.5168	0.5168
GTRG	44	-743.7321	1594.0558	0.3618	0.8786
HKYI	40	-751.6035	1598.3222	0.0429	0.9215
GTRI	44	-746.3449	1599.2814	0.0265	0.9480
HKYIG	41	-750.7458	1599.4361	0.0246	0.9726
GTRIG	45	-745.1366	1599.8016	0.0205	0.9930
HKY	39	-756.0002	1604.3124	0.0021	0.9952
K2PG	37	-759.1040	1604.9898	0.0015	0.9967
GTR	43	-750.6915	1605.0652	0.0015	0.9982
SYMG	41	-754.0052	1605.9549	0.0009	0.9991
SYMI	41	-755.1752	1608.2948	0.0003	0.9994
K2PI	37	-760.9349	1608.6517	0.0002	0.9997
SYMIG	42	-754.2808	1609.3616	0.0002	0.9998
K2PIG	38	-760.1455	1609.8252	0.0001	1.0000
F81G	39	-760.4299	1613.1717	0.0000	1.0000
K2P	36	-766.5096	1617.0735	0.0000	1.0000
SYM	40	-761.7356	1618.5864	0.0000	1.0000
F81I	39	-763.4266	1619.1650	0.0000	1.0000
F81IG	40	-762.7179	1620.5509	0.0000	1.0000
F81	38	-766.9786	1623.4914	0.0000	1.0000
JC69G	36	-770.0757	1624.2058	0.0000	1.0000
JC69I	36	-772.5434	1629.1412	0.0000	1.0000
JC69IG	37	-771.8356	1630.4531	0.0000	1.0000
JC69	35	-776.8639	1635.0792	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-743.7321	1575.4642	0.6857	0.6857
HKYG	40	-749.1139	1578.2278	0.1722	0.8579
GTRIG	45	-745.1366	1580.2733	0.0619	0.9198
GTRI	44	-746.3449	1580.6898	0.0503	0.9701
HKYI	40	-751.6035	1583.2070	0.0143	0.9844
HKYIG	41	-750.7458	1583.4917	0.0124	0.9968
GTR	43	-750.6915	1587.3830	0.0018	0.9986
HKY	39	-756.0002	1590.0005	0.0005	0.9990
SYMG	41	-754.0052	1590.0104	0.0005	0.9995
K2PG	37	-759.1040	1592.2080	0.0002	0.9997
SYMI	41	-755.1752	1592.3504	0.0001	0.9998
SYMIG	42	-754.2808	1592.5616	0.0001	0.9999
K2PI	37	-760.9349	1595.8699	0.0000	1.0000
K2PIG	38	-760.1455	1596.2910	0.0000	1.0000
F81G	39	-760.4299	1598.8598	0.0000	1.0000
SYM	40	-761.7356	1603.4712	0.0000	1.0000
F81I	39	-763.4266	1604.8531	0.0000	1.0000
K2P	36	-766.5096	1605.0192	0.0000	1.0000
F81IG	40	-762.7179	1605.4357	0.0000	1.0000
F81	38	-766.9786	1609.9572	0.0000	1.0000
JC69G	36	-770.0757	1612.1515	0.0000	1.0000
JC69I	36	-772.5434	1617.0869	0.0000	1.0000
JC69IG	37	-771.8356	1617.6713	0.0000	1.0000
JC69	35	-776.8639	1623.7279	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-749.1139	1720.3461	0.7449	0.7449
K2PG	37	-759.1040	1723.6675	0.1415	0.8864
HKYI	40	-751.6035	1725.3254	0.0618	0.9482
K2PI	37	-760.9349	1727.3294	0.0227	0.9709
HKY	39	-756.0002	1728.5659	0.0122	0.9831
HKYIG	41	-750.7458	1729.1630	0.0091	0.9921
K2PIG	38	-760.1455	1731.3034	0.0031	0.9953
GTRG	44	-743.7321	1731.7944	0.0024	0.9977
K2P	36	-766.5096	1732.9257	0.0014	0.9991
SYMG	41	-754.0052	1735.6818	0.0003	0.9994
GTRI	44	-746.3449	1737.0201	0.0002	0.9996
F81G	39	-760.4299	1737.4252	0.0001	0.9997
SYMI	41	-755.1752	1738.0217	0.0001	0.9999
JC69G	36	-770.0757	1740.0580	0.0000	0.9999
GTRIG	45	-745.1366	1740.1565	0.0000	0.9999
GTR	43	-750.6915	1740.1602	0.0000	1.0000
SYMIG	42	-754.2808	1741.7859	0.0000	1.0000
F81I	39	-763.4266	1743.4185	0.0000	1.0000
F81	38	-766.9786	1744.9697	0.0000	1.0000
JC69I	36	-772.5434	1744.9934	0.0000	1.0000
SYM	40	-761.7356	1745.5896	0.0000	1.0000
F81IG	40	-762.7179	1747.5541	0.0000	1.0000
JC69	35	-776.8639	1748.0814	0.0000	1.0000
JC69IG	37	-771.8356	1749.1308	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/chr2_11187.phylip = 1 - 258;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11187.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11187.phylip = 1 - 258;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11187.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/chr2_11187.phylip = 1 - 258;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11187.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

