
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:34 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/chr1_7424.phylip" (19 taxa, 188 characters)

Minimum AIC  model: HKYI
Minimum AICc model: K2PI
Minimum BIC  model: K2PI


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
K2PI	37	-420.9911	934.7289	0.3967	0.3967
K2PG	37	-421.7378	936.2223	0.1880	0.5847
HKYI	40	-416.9714	936.2556	0.1849	0.7695
HKYG	40	-417.5697	937.4524	0.1016	0.8712
K2PIG	38	-420.9917	937.8760	0.0822	0.9534
HKYIG	41	-416.9718	939.5327	0.0359	0.9893
SYMI	41	-418.9414	943.4719	0.0050	0.9943
SYMG	41	-419.5390	944.6671	0.0028	0.9971
GTRI	44	-415.5235	946.7393	0.0010	0.9981
SYMIG	42	-418.9423	946.7950	0.0010	0.9990
GTRG	44	-416.0280	947.7483	0.0006	0.9996
GTRIG	45	-415.5242	950.2033	0.0002	0.9998
K2P	36	-430.7776	951.1976	0.0001	0.9999
HKY	39	-426.3853	951.8517	0.0001	1.0000
JC69I	36	-433.0590	955.7603	0.0000	1.0000
JC69G	36	-433.5582	956.7587	0.0000	1.0000
F81I	39	-429.1889	957.4589	0.0000	1.0000
F81G	39	-429.6468	958.3747	0.0000	1.0000
JC69IG	37	-433.0591	958.8649	0.0000	1.0000
SYM	40	-428.3031	958.9191	0.0000	1.0000
F81IG	40	-429.1891	960.6912	0.0000	1.0000
GTR	43	-424.4753	961.2284	0.0000	1.0000
JC69	35	-442.1416	970.8621	0.0000	1.0000
F81	38	-438.1356	972.1638	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-416.9714	913.9427	0.3529	0.3529
HKYG	40	-417.5697	915.1394	0.1940	0.5468
HKYIG	41	-416.9718	915.9437	0.1297	0.6766
K2PI	37	-420.9911	915.9823	0.1273	0.8039
K2PG	37	-421.7378	917.4757	0.0603	0.8642
K2PIG	38	-420.9917	917.9833	0.0468	0.9110
GTRI	44	-415.5235	919.0470	0.0275	0.9385
SYMI	41	-418.9414	919.8828	0.0181	0.9566
GTRG	44	-416.0280	920.0560	0.0166	0.9732
GTRIG	45	-415.5242	921.0483	0.0101	0.9833
SYMG	41	-419.5390	921.0780	0.0100	0.9932
SYMIG	42	-418.9423	921.8847	0.0067	0.9999
HKY	39	-426.3853	930.7707	0.0001	1.0000
K2P	36	-430.7776	933.5552	0.0000	1.0000
GTR	43	-424.4753	934.9506	0.0000	1.0000
F81I	39	-429.1889	936.3778	0.0000	1.0000
SYM	40	-428.3031	936.6062	0.0000	1.0000
F81G	39	-429.6468	937.2936	0.0000	1.0000
JC69I	36	-433.0590	938.1179	0.0000	1.0000
F81IG	40	-429.1891	938.3782	0.0000	1.0000
JC69G	36	-433.5582	939.1163	0.0000	1.0000
JC69IG	37	-433.0591	940.1182	0.0000	1.0000
F81	38	-438.1356	952.2711	0.0000	1.0000
JC69	35	-442.1416	954.2831	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-420.9911	1035.7306	0.6316	0.6316
K2PG	37	-421.7378	1037.2240	0.2994	0.9310
K2PIG	38	-420.9917	1040.9681	0.0460	0.9770
HKYI	40	-416.9714	1043.4004	0.0136	0.9907
HKYG	40	-417.5697	1044.5971	0.0075	0.9982
HKYIG	41	-416.9718	1048.6378	0.0010	0.9992
K2P	36	-430.7776	1050.0672	0.0005	0.9997
SYMI	41	-418.9414	1052.5770	0.0001	0.9998
SYMG	41	-419.5390	1053.7722	0.0001	0.9999
JC69I	36	-433.0590	1054.6298	0.0000	0.9999
JC69G	36	-433.5582	1055.6282	0.0000	1.0000
HKY	39	-426.3853	1056.9919	0.0000	1.0000
SYMIG	42	-418.9423	1057.8152	0.0000	1.0000
JC69IG	37	-433.0591	1059.8666	0.0000	1.0000
GTRI	44	-415.5235	1061.4504	0.0000	1.0000
GTRG	44	-416.0280	1062.4595	0.0000	1.0000
F81I	39	-429.1889	1062.5991	0.0000	1.0000
F81G	39	-429.6468	1063.5148	0.0000	1.0000
SYM	40	-428.3031	1066.0639	0.0000	1.0000
GTRIG	45	-415.5242	1066.6882	0.0000	1.0000
JC69	35	-442.1416	1067.5586	0.0000	1.0000
F81IG	40	-429.1891	1067.8359	0.0000	1.0000
GTR	43	-424.4753	1074.1176	0.0000	1.0000
F81	38	-438.1356	1075.2559	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7424.phylip = 1 - 188;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7424.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7424.phylip = 1 - 188;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7424.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7424.phylip = 1 - 188;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_7424.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

