
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:15 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/chr4_10598.phylip" (19 taxa, 780 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	-3124.4260	6333.2904	0.5351	0.5351
HKYIG	41	-3124.1702	6335.0071	0.2268	0.7619
GTRIG	45	-3120.3411	6336.3225	0.1175	0.8794
GTRG	44	-3121.4854	6336.3586	0.1154	0.9948
HKYI	40	-3129.5544	6343.5473	0.0032	0.9980
GTRI	44	-3125.5252	6344.4382	0.0020	1.0000
SYMG	41	-3136.8738	6360.4142	0.0000	1.0000
SYMIG	42	-3135.9666	6360.8341	0.0000	1.0000
K2PG	37	-3142.8440	6363.4778	0.0000	1.0000
K2PIG	38	-3142.1209	6364.2417	0.0000	1.0000
SYMI	41	-3144.2670	6375.2006	0.0000	1.0000
K2PI	37	-3149.3208	6376.4314	0.0000	1.0000
F81G	39	-3215.6850	6513.5863	0.0000	1.0000
F81IG	40	-3215.8382	6516.1148	0.0000	1.0000
F81I	39	-3219.5151	6521.2464	0.0000	1.0000
JC69G	36	-3231.6193	6538.8240	0.0000	1.0000
JC69IG	37	-3231.5994	6540.9886	0.0000	1.0000
JC69I	36	-3235.8827	6547.3509	0.0000	1.0000
GTR	43	-3246.2328	6583.6069	0.0000	1.0000
HKY	39	-3250.8434	6583.9029	0.0000	1.0000
SYM	40	-3262.8359	6610.1103	0.0000	1.0000
K2P	36	-3269.6779	6614.9413	0.0000	1.0000
F81	38	-3335.0090	6750.0181	0.0000	1.0000
JC69	35	-3350.5518	6774.4908	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-3124.4260	6328.8520	0.4476	0.4476
HKYIG	41	-3124.1702	6330.3404	0.2126	0.6602
GTRIG	45	-3120.3411	6330.6822	0.1792	0.8395
GTRG	44	-3121.4854	6330.9709	0.1552	0.9946
GTRI	44	-3125.5252	6339.0504	0.0027	0.9973
HKYI	40	-3129.5544	6339.1089	0.0027	1.0000
SYMG	41	-3136.8738	6355.7475	0.0000	1.0000
SYMIG	42	-3135.9666	6355.9332	0.0000	1.0000
K2PG	37	-3142.8440	6359.6880	0.0000	1.0000
K2PIG	38	-3142.1209	6360.2417	0.0000	1.0000
SYMI	41	-3144.2670	6370.5339	0.0000	1.0000
K2PI	37	-3149.3208	6372.6416	0.0000	1.0000
F81G	39	-3215.6850	6509.3701	0.0000	1.0000
F81IG	40	-3215.8382	6511.6763	0.0000	1.0000
F81I	39	-3219.5151	6517.0302	0.0000	1.0000
JC69G	36	-3231.6193	6535.2385	0.0000	1.0000
JC69IG	37	-3231.5994	6537.1988	0.0000	1.0000
JC69I	36	-3235.8827	6543.7654	0.0000	1.0000
GTR	43	-3246.2328	6578.4656	0.0000	1.0000
HKY	39	-3250.8434	6579.6867	0.0000	1.0000
SYM	40	-3262.8359	6605.6718	0.0000	1.0000
K2P	36	-3269.6779	6611.3559	0.0000	1.0000
F81	38	-3335.0090	6746.0181	0.0000	1.0000
JC69	35	-3350.5518	6771.1037	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3124.4260	6515.2237	0.9502	0.9502
HKYIG	41	-3124.1702	6521.3715	0.0439	0.9941
HKYI	40	-3129.5544	6525.4806	0.0056	0.9997
K2PG	37	-3142.8440	6532.0819	0.0002	1.0000
GTRG	44	-3121.4854	6535.9798	0.0000	1.0000
K2PIG	38	-3142.1209	6537.2949	0.0000	1.0000
GTRIG	45	-3120.3411	6540.3504	0.0000	1.0000
GTRI	44	-3125.5252	6544.0594	0.0000	1.0000
K2PI	37	-3149.3208	6545.0355	0.0000	1.0000
SYMG	41	-3136.8738	6546.7786	0.0000	1.0000
SYMIG	42	-3135.9666	6551.6235	0.0000	1.0000
SYMI	41	-3144.2670	6561.5650	0.0000	1.0000
F81G	39	-3215.6850	6691.0825	0.0000	1.0000
F81IG	40	-3215.8382	6698.0481	0.0000	1.0000
F81I	39	-3219.5151	6698.7426	0.0000	1.0000
JC69G	36	-3231.6193	6702.9731	0.0000	1.0000
JC69IG	37	-3231.5994	6709.5927	0.0000	1.0000
JC69I	36	-3235.8827	6711.5000	0.0000	1.0000
HKY	39	-3250.8434	6761.3992	0.0000	1.0000
GTR	43	-3246.2328	6778.8153	0.0000	1.0000
K2P	36	-3269.6779	6779.0904	0.0000	1.0000
SYM	40	-3262.8359	6792.0436	0.0000	1.0000
F81	38	-3335.0090	6923.0712	0.0000	1.0000
JC69	35	-3350.5518	6934.1790	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/chr4_10598.phylip = 1 - 780;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10598.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/chr4_10598.phylip = 1 - 780;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10598.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/chr4_10598.phylip = 1 - 780;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10598.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

