
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:17 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/chrZ_7416.phylip" (19 taxa, 312 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	-806.9543	1706.0119	0.4450	0.4450
HKYI	40	-807.3895	1706.8824	0.2880	0.7329
HKYIG	41	-806.7807	1708.3170	0.1405	0.8735
GTRG	44	-803.6734	1710.1783	0.0554	0.9289
GTRI	44	-804.0901	1711.0117	0.0365	0.9654
GTRIG	45	-803.0896	1711.7431	0.0253	0.9908
K2PG	37	-815.5740	1715.4108	0.0040	0.9948
K2PI	37	-815.9253	1716.1135	0.0028	0.9977
K2PIG	38	-815.4143	1717.6857	0.0013	0.9990
HKY	39	-815.0243	1719.5191	0.0005	0.9995
SYMG	41	-813.2116	1721.1788	0.0002	0.9997
SYMI	41	-813.5461	1721.8478	0.0002	0.9999
SYMIG	42	-812.9524	1723.3322	0.0001	0.9999
GTR	43	-811.8825	1723.8844	0.0001	1.0000
K2P	36	-823.5443	1728.7759	0.0000	1.0000
SYM	40	-820.9113	1733.9259	0.0000	1.0000
F81G	39	-833.6485	1756.7676	0.0000	1.0000
F81I	39	-833.8608	1757.1921	0.0000	1.0000
F81IG	40	-833.6059	1759.3152	0.0000	1.0000
JC69G	36	-841.4319	1764.5511	0.0000	1.0000
JC69I	36	-841.6403	1764.9679	0.0000	1.0000
JC69IG	37	-841.3874	1767.0375	0.0000	1.0000
F81	38	-840.9317	1768.7205	0.0000	1.0000
JC69	35	-848.5724	1776.2751	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-806.9543	1693.9085	0.3101	0.3101
HKYI	40	-807.3895	1694.7790	0.2007	0.5108
GTRG	44	-803.6734	1695.3468	0.1511	0.6618
HKYIG	41	-806.7807	1695.5615	0.1357	0.7975
GTRIG	45	-803.0896	1696.1792	0.0996	0.8972
GTRI	44	-804.0901	1696.1802	0.0996	0.9967
K2PG	37	-815.5740	1705.1480	0.0011	0.9979
K2PI	37	-815.9253	1705.8507	0.0008	0.9987
K2PIG	38	-815.4143	1706.8285	0.0005	0.9991
HKY	39	-815.0243	1708.0485	0.0003	0.9994
SYMG	41	-813.2116	1708.4232	0.0002	0.9996
SYMI	41	-813.5461	1709.0922	0.0002	0.9998
GTR	43	-811.8825	1709.7650	0.0001	0.9999
SYMIG	42	-812.9524	1709.9047	0.0001	1.0000
K2P	36	-823.5443	1719.0886	0.0000	1.0000
SYM	40	-820.9113	1721.8226	0.0000	1.0000
F81G	39	-833.6485	1745.2970	0.0000	1.0000
F81I	39	-833.8608	1745.7215	0.0000	1.0000
F81IG	40	-833.6059	1747.2119	0.0000	1.0000
JC69G	36	-841.4319	1754.8638	0.0000	1.0000
JC69I	36	-841.6403	1755.2807	0.0000	1.0000
JC69IG	37	-841.3874	1756.7747	0.0000	1.0000
F81	38	-840.9317	1757.8633	0.0000	1.0000
JC69	35	-848.5724	1767.1447	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-806.9543	1843.6287	0.2867	0.2867
K2PG	37	-815.5740	1843.6391	0.2852	0.5720
K2PI	37	-815.9253	1844.3418	0.2007	0.7727
HKYI	40	-807.3895	1844.4992	0.1855	0.9582
HKYIG	41	-806.7807	1849.0246	0.0193	0.9775
K2PIG	38	-815.4143	1849.0627	0.0189	0.9965
K2P	36	-823.5443	1853.8367	0.0017	0.9982
HKY	39	-815.0243	1854.0256	0.0016	0.9998
GTRG	44	-803.6734	1860.0390	0.0001	0.9999
GTRI	44	-804.0901	1860.8723	0.0001	0.9999
SYMG	41	-813.2116	1861.8863	0.0000	1.0000
SYMI	41	-813.5461	1862.5554	0.0000	1.0000
GTRIG	45	-803.0896	1864.6143	0.0000	1.0000
SYMIG	42	-812.9524	1867.1108	0.0000	1.0000
GTR	43	-811.8825	1870.7142	0.0000	1.0000
SYM	40	-820.9113	1871.5427	0.0000	1.0000
JC69G	36	-841.4319	1889.6119	0.0000	1.0000
JC69I	36	-841.6403	1890.0288	0.0000	1.0000
F81G	39	-833.6485	1891.2741	0.0000	1.0000
F81I	39	-833.8608	1891.6987	0.0000	1.0000
JC69IG	37	-841.3874	1895.2658	0.0000	1.0000
F81IG	40	-833.6059	1896.9320	0.0000	1.0000
JC69	35	-848.5724	1898.1498	0.0000	1.0000
F81	38	-840.9317	1900.0975	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/chrZ_7416.phylip = 1 - 312;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7416.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/chrZ_7416.phylip = 1 - 312;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7416.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/chrZ_7416.phylip = 1 - 312;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7416.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

