
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:31 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/chr6_8064.phylip" (19 taxa, 578 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-1042.7512	2180.9320	0.2731	0.2731
GTRG	44	-1042.7840	2180.9975	0.2643	0.5375
HKYI	40	-1047.9198	2181.9475	0.1644	0.7018
HKYG	40	-1048.0277	2182.1634	0.1476	0.8494
GTRIG	45	-1042.7376	2183.2572	0.0854	0.9348
HKYIG	41	-1047.8609	2184.1472	0.0547	0.9895
GTR	43	-1047.5489	2188.1839	0.0073	0.9968
HKY	39	-1053.0202	2189.8396	0.0032	1.0000
F81I	39	-1060.0959	2203.9910	0.0000	1.0000
F81G	39	-1060.2667	2204.3327	0.0000	1.0000
F81IG	40	-1060.0312	2206.1704	0.0000	1.0000
F81	38	-1065.4389	2212.3768	0.0000	1.0000
K2PI	37	-1076.5968	2232.4010	0.0000	1.0000
K2PG	37	-1076.9165	2233.0405	0.0000	1.0000
K2PIG	38	-1076.4951	2234.4893	0.0000	1.0000
SYMI	41	-1073.4447	2235.3149	0.0000	1.0000
SYMG	41	-1073.5995	2235.6244	0.0000	1.0000
SYMIG	42	-1073.4062	2237.5638	0.0000	1.0000
K2P	36	-1082.4443	2241.8128	0.0000	1.0000
SYM	40	-1078.7380	2243.5840	0.0000	1.0000
JC69I	36	-1087.7452	2252.4145	0.0000	1.0000
JC69G	36	-1088.0205	2252.9653	0.0000	1.0000
JC69IG	37	-1087.6732	2254.5538	0.0000	1.0000
JC69	35	-1093.4547	2261.5588	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1042.7512	2173.5024	0.3247	0.3247
GTRG	44	-1042.7840	2173.5679	0.3143	0.6390
GTRIG	45	-1042.7376	2175.4753	0.1211	0.7601
HKYI	40	-1047.9198	2175.8395	0.1009	0.8611
HKYG	40	-1048.0277	2176.0554	0.0906	0.9517
HKYIG	41	-1047.8609	2177.7218	0.0394	0.9910
GTR	43	-1047.5489	2181.0978	0.0073	0.9983
HKY	39	-1053.0202	2184.0403	0.0017	1.0000
F81I	39	-1060.0959	2198.1918	0.0000	1.0000
F81G	39	-1060.2667	2198.5334	0.0000	1.0000
F81IG	40	-1060.0312	2200.0624	0.0000	1.0000
F81	38	-1065.4389	2206.8778	0.0000	1.0000
K2PI	37	-1076.5968	2227.1936	0.0000	1.0000
K2PG	37	-1076.9165	2227.8331	0.0000	1.0000
SYMI	41	-1073.4447	2228.8895	0.0000	1.0000
K2PIG	38	-1076.4951	2228.9902	0.0000	1.0000
SYMG	41	-1073.5995	2229.1990	0.0000	1.0000
SYMIG	42	-1073.4062	2230.8124	0.0000	1.0000
K2P	36	-1082.4443	2236.8886	0.0000	1.0000
SYM	40	-1078.7380	2237.4760	0.0000	1.0000
JC69I	36	-1087.7452	2247.4903	0.0000	1.0000
JC69G	36	-1088.0205	2248.0411	0.0000	1.0000
JC69IG	37	-1087.6732	2249.3464	0.0000	1.0000
JC69	35	-1093.4547	2256.9094	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1047.9198	2350.2225	0.4785	0.4785
HKYG	40	-1048.0277	2350.4384	0.4296	0.9081
HKY	39	-1053.0202	2354.0637	0.0701	0.9782
HKYIG	41	-1047.8609	2356.4643	0.0211	0.9993
GTRI	44	-1042.7512	2365.3236	0.0003	0.9996
GTRG	44	-1042.7840	2365.3892	0.0002	0.9998
F81I	39	-1060.0959	2368.2152	0.0001	0.9999
F81G	39	-1060.2667	2368.5568	0.0000	0.9999
GTR	43	-1047.5489	2368.5595	0.0000	1.0000
GTRIG	45	-1042.7376	2371.6561	0.0000	1.0000
F81	38	-1065.4389	2372.5416	0.0000	1.0000
F81IG	40	-1060.0312	2374.4454	0.0000	1.0000
K2PI	37	-1076.5968	2388.4979	0.0000	1.0000
K2PG	37	-1076.9165	2389.1373	0.0000	1.0000
K2P	36	-1082.4443	2393.8333	0.0000	1.0000
K2PIG	38	-1076.4951	2394.6540	0.0000	1.0000
JC69I	36	-1087.7452	2404.4350	0.0000	1.0000
JC69G	36	-1088.0205	2404.9857	0.0000	1.0000
SYMI	41	-1073.4447	2407.6320	0.0000	1.0000
SYMG	41	-1073.5995	2407.9415	0.0000	1.0000
JC69	35	-1093.4547	2409.4944	0.0000	1.0000
JC69IG	37	-1087.6732	2410.6506	0.0000	1.0000
SYM	40	-1078.7380	2411.8590	0.0000	1.0000
SYMIG	42	-1073.4062	2413.9145	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8064.phylip = 1 - 578;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8064.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8064.phylip = 1 - 578;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8064.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8064.phylip = 1 - 578;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_8064.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;


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End of Output

