
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:30 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/chr22_865.phylip" (19 taxa, 364 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	-1049.2253	2198.8644	0.4650	0.4650
GTRG	44	-1049.5473	2199.5083	0.3370	0.8020
GTRIG	45	-1049.2293	2201.4774	0.1259	0.9279
HKYI	40	-1056.9336	2204.0221	0.0353	0.9632
HKYG	40	-1057.2111	2204.5771	0.0267	0.9899
HKYIG	41	-1056.9363	2206.5684	0.0099	0.9998
GTR	43	-1058.5974	2215.0197	0.0001	0.9999
SYMI	41	-1062.9006	2218.4969	0.0000	1.0000
SYMG	41	-1063.4524	2219.6004	0.0000	1.0000
HKY	39	-1066.4475	2220.5245	0.0000	1.0000
K2PI	37	-1069.6581	2221.9419	0.0000	1.0000
SYMIG	42	-1063.4523	2222.1570	0.0000	1.0000
K2PG	37	-1069.9846	2222.5949	0.0000	1.0000
K2PIG	38	-1069.9845	2225.0889	0.0000	1.0000
SYM	40	-1072.9091	2235.9730	0.0000	1.0000
K2P	36	-1080.4712	2241.0892	0.0000	1.0000
F81I	39	-1092.4862	2272.6021	0.0000	1.0000
F81G	39	-1092.6956	2273.0208	0.0000	1.0000
F81IG	40	-1092.7260	2275.6068	0.0000	1.0000
JC69I	36	-1103.8288	2287.8044	0.0000	1.0000
JC69G	36	-1104.1435	2288.4338	0.0000	1.0000
F81	38	-1102.1738	2289.4675	0.0000	1.0000
JC69IG	37	-1104.1975	2291.0208	0.0000	1.0000
JC69	35	-1113.9115	2305.5059	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1049.2253	2186.4506	0.4665	0.4665
GTRG	44	-1049.5473	2187.0945	0.3381	0.8046
GTRIG	45	-1049.2293	2188.4586	0.1709	0.9756
HKYI	40	-1056.9336	2193.8673	0.0114	0.9870
HKYG	40	-1057.2111	2194.4223	0.0087	0.9957
HKYIG	41	-1056.9363	2195.8727	0.0042	0.9999
GTR	43	-1058.5974	2203.1947	0.0001	1.0000
SYMI	41	-1062.9006	2207.8012	0.0000	1.0000
SYMG	41	-1063.4524	2208.9048	0.0000	1.0000
HKY	39	-1066.4475	2210.8949	0.0000	1.0000
SYMIG	42	-1063.4523	2210.9046	0.0000	1.0000
K2PI	37	-1069.6581	2213.3161	0.0000	1.0000
K2PG	37	-1069.9846	2213.9692	0.0000	1.0000
K2PIG	38	-1069.9845	2215.9689	0.0000	1.0000
SYM	40	-1072.9091	2225.8182	0.0000	1.0000
K2P	36	-1080.4712	2232.9424	0.0000	1.0000
F81I	39	-1092.4862	2262.9724	0.0000	1.0000
F81G	39	-1092.6956	2263.3912	0.0000	1.0000
F81IG	40	-1092.7260	2265.4520	0.0000	1.0000
JC69I	36	-1103.8288	2279.6576	0.0000	1.0000
JC69G	36	-1104.1435	2280.2870	0.0000	1.0000
F81	38	-1102.1738	2280.3475	0.0000	1.0000
JC69IG	37	-1104.1975	2282.3950	0.0000	1.0000
JC69	35	-1113.9115	2297.8230	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1056.9336	2349.7535	0.5325	0.5325
HKYG	40	-1057.2111	2350.3084	0.4035	0.9360
HKYIG	41	-1056.9363	2355.6560	0.0278	0.9638
K2PI	37	-1069.6581	2357.5108	0.0110	0.9749
GTRI	44	-1049.2253	2357.9253	0.0090	0.9838
K2PG	37	-1069.9846	2358.1639	0.0079	0.9917
GTRG	44	-1049.5473	2358.5693	0.0065	0.9982
HKY	39	-1066.4475	2362.8839	0.0008	0.9990
GTRIG	45	-1049.2293	2363.8305	0.0005	0.9994
K2PIG	38	-1069.9845	2364.0608	0.0004	0.9999
SYMI	41	-1062.9006	2367.5845	0.0001	0.9999
SYMG	41	-1063.4524	2368.6881	0.0000	1.0000
GTR	43	-1058.5974	2370.7723	0.0000	1.0000
K2P	36	-1080.4712	2373.2400	0.0000	1.0000
SYMIG	42	-1063.4523	2374.5851	0.0000	1.0000
SYM	40	-1072.9091	2381.7044	0.0000	1.0000
F81I	39	-1092.4862	2414.9614	0.0000	1.0000
F81G	39	-1092.6956	2415.3802	0.0000	1.0000
JC69I	36	-1103.8288	2419.9552	0.0000	1.0000
JC69G	36	-1104.1435	2420.5846	0.0000	1.0000
F81IG	40	-1092.7260	2421.3381	0.0000	1.0000
JC69IG	37	-1104.1975	2426.5897	0.0000	1.0000
F81	38	-1102.1738	2428.4394	0.0000	1.0000
JC69	35	-1113.9115	2434.2234	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/chr22_865.phylip = 1 - 364;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_865.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/chr22_865.phylip = 1 - 364;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_865.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/chr22_865.phylip = 1 - 364;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr22_865.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

