
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:16 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_7577.phylip" (19 taxa, 736 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2183.8287	4461.3882	0.6374	0.6374
GTRIG	45	-2183.5787	4463.1574	0.2632	0.9006
GTRI	44	-2185.8686	4465.4679	0.0829	0.9835
HKYG	40	-2192.4551	4469.6297	0.0103	0.9938
HKYIG	41	-2192.2580	4471.4786	0.0041	0.9979
HKYI	40	-2194.0509	4472.8213	0.0021	1.0000
SYMG	41	-2208.7270	4504.4164	0.0000	1.0000
GTR	43	-2206.5335	4504.5353	0.0000	1.0000
K2PG	37	-2213.8319	4505.6924	0.0000	1.0000
SYMIG	42	-2208.4740	4506.1600	0.0000	1.0000
K2PIG	38	-2213.6075	4507.4676	0.0000	1.0000
SYMI	41	-2210.5738	4508.1101	0.0000	1.0000
K2PI	37	-2215.3373	4508.7032	0.0000	1.0000
HKY	39	-2215.3764	4513.2356	0.0000	1.0000
SYM	40	-2231.0139	4546.7473	0.0000	1.0000
K2P	36	-2237.4893	4550.7898	0.0000	1.0000
F81G	39	-2249.6565	4581.7958	0.0000	1.0000
F81IG	40	-2249.4434	4583.6063	0.0000	1.0000
F81I	39	-2251.1552	4584.7931	0.0000	1.0000
JC69G	36	-2266.7737	4609.3586	0.0000	1.0000
JC69IG	37	-2266.4876	4611.0038	0.0000	1.0000
JC69I	36	-2268.4595	4612.7302	0.0000	1.0000
F81	38	-2272.0976	4624.4478	0.0000	1.0000
JC69	35	-2289.9271	4653.4542	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2183.8287	4455.6574	0.6178	0.6178
GTRIG	45	-2183.5787	4457.1574	0.2918	0.9097
GTRI	44	-2185.8686	4459.7371	0.0803	0.9900
HKYG	40	-2192.4551	4464.9103	0.0060	0.9961
HKYIG	41	-2192.2580	4466.5161	0.0027	0.9988
HKYI	40	-2194.0509	4468.1019	0.0012	1.0000
GTR	43	-2206.5335	4499.0671	0.0000	1.0000
SYMG	41	-2208.7270	4499.4539	0.0000	1.0000
SYMIG	42	-2208.4740	4500.9479	0.0000	1.0000
K2PG	37	-2213.8319	4501.6638	0.0000	1.0000
SYMI	41	-2210.5738	4503.1475	0.0000	1.0000
K2PIG	38	-2213.6075	4503.2150	0.0000	1.0000
K2PI	37	-2215.3373	4504.6745	0.0000	1.0000
HKY	39	-2215.3764	4508.7529	0.0000	1.0000
SYM	40	-2231.0139	4542.0279	0.0000	1.0000
K2P	36	-2237.4893	4546.9786	0.0000	1.0000
F81G	39	-2249.6565	4577.3130	0.0000	1.0000
F81IG	40	-2249.4434	4578.8869	0.0000	1.0000
F81I	39	-2251.1552	4580.3104	0.0000	1.0000
JC69G	36	-2266.7737	4605.5474	0.0000	1.0000
JC69IG	37	-2266.4876	4606.9751	0.0000	1.0000
JC69I	36	-2268.4595	4608.9191	0.0000	1.0000
F81	38	-2272.0976	4620.1953	0.0000	1.0000
JC69	35	-2289.9271	4649.8542	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2192.4551	4648.9595	0.7938	0.7938
HKYI	40	-2194.0509	4652.1511	0.1609	0.9547
HKYIG	41	-2192.2580	4655.1665	0.0356	0.9904
GTRG	44	-2183.8287	4658.1115	0.0082	0.9985
GTRI	44	-2185.8686	4662.1912	0.0011	0.9996
GTRIG	45	-2183.5787	4664.2127	0.0004	1.0000
K2PG	37	-2213.8319	4671.9093	0.0000	1.0000
K2PI	37	-2215.3373	4674.9201	0.0000	1.0000
K2PIG	38	-2213.6075	4678.0618	0.0000	1.0000
SYMG	41	-2208.7270	4688.1043	0.0000	1.0000
HKY	39	-2215.3764	4688.2009	0.0000	1.0000
SYMI	41	-2210.5738	4691.7980	0.0000	1.0000
SYMIG	42	-2208.4740	4694.1996	0.0000	1.0000
GTR	43	-2206.5335	4696.9200	0.0000	1.0000
K2P	36	-2237.4893	4712.6229	0.0000	1.0000
SYM	40	-2231.0139	4726.0771	0.0000	1.0000
F81G	39	-2249.6565	4756.7610	0.0000	1.0000
F81I	39	-2251.1552	4759.7583	0.0000	1.0000
F81IG	40	-2249.4434	4762.9361	0.0000	1.0000
JC69G	36	-2266.7737	4771.1917	0.0000	1.0000
JC69I	36	-2268.4595	4774.5634	0.0000	1.0000
JC69IG	37	-2266.4876	4777.2207	0.0000	1.0000
F81	38	-2272.0976	4795.0420	0.0000	1.0000
JC69	35	-2289.9271	4810.8973	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/chr4_7577.phylip = 1 - 736;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7577.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7577.phylip = 1 - 736;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7577.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 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_7577.phylip = 1 - 736;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7577.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;


-------------------------------------------------------------
End of Output

