
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:14 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_32334.phylip" (19 taxa, 770 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	-2092.3885	4278.2391	0.7028	0.7028
GTRI	44	-2093.4045	4280.2711	0.2545	0.9573
GTRIG	45	-2094.4671	4284.6525	0.0285	0.9857
HKYG	40	-2101.1255	4286.7503	0.0100	0.9957
HKYI	40	-2102.0652	4288.6298	0.0039	0.9996
HKYIG	41	-2103.2503	4293.2313	0.0004	1.0000
K2PG	37	-2120.7760	4319.3935	0.0000	1.0000
SYMG	41	-2116.6103	4319.9515	0.0000	1.0000
SYMIG	42	-2116.2866	4321.5416	0.0000	1.0000
K2PIG	38	-2122.8022	4325.6590	0.0000	1.0000
K2PI	37	-2124.5099	4326.8613	0.0000	1.0000
SYMI	41	-2120.5225	4327.7757	0.0000	1.0000
F81G	39	-2129.6285	4341.5310	0.0000	1.0000
GTR	43	-2125.4517	4342.1155	0.0000	1.0000
F81IG	40	-2129.3587	4343.2167	0.0000	1.0000
F81I	39	-2130.5230	4343.3200	0.0000	1.0000
HKY	39	-2132.2179	4346.7097	0.0000	1.0000
JC69G	36	-2147.1946	4370.0236	0.0000	1.0000
JC69IG	37	-2146.9225	4371.6865	0.0000	1.0000
K2P	36	-2150.9427	4377.5198	0.0000	1.0000
SYM	40	-2147.0400	4378.5794	0.0000	1.0000
JC69I	36	-2151.4902	4378.6147	0.0000	1.0000
F81	38	-2158.7965	4397.6476	0.0000	1.0000
JC69	35	-2175.9417	4425.3167	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2092.3885	4272.7770	0.7039	0.7039
GTRI	44	-2093.4045	4274.8090	0.2548	0.9588
GTRIG	45	-2094.4671	4278.9342	0.0324	0.9911
HKYG	40	-2101.1255	4282.2510	0.0062	0.9973
HKYI	40	-2102.0652	4284.1304	0.0024	0.9997
HKYIG	41	-2103.2503	4288.5006	0.0003	1.0000
SYMG	41	-2116.6103	4315.2207	0.0000	1.0000
K2PG	37	-2120.7760	4315.5520	0.0000	1.0000
SYMIG	42	-2116.2866	4316.5732	0.0000	1.0000
K2PIG	38	-2122.8022	4321.6043	0.0000	1.0000
K2PI	37	-2124.5099	4323.0198	0.0000	1.0000
SYMI	41	-2120.5225	4323.0450	0.0000	1.0000
GTR	43	-2125.4517	4336.9034	0.0000	1.0000
F81G	39	-2129.6285	4337.2570	0.0000	1.0000
F81IG	40	-2129.3587	4338.7174	0.0000	1.0000
F81I	39	-2130.5230	4339.0460	0.0000	1.0000
HKY	39	-2132.2179	4342.4357	0.0000	1.0000
JC69G	36	-2147.1946	4366.3892	0.0000	1.0000
JC69IG	37	-2146.9225	4367.8450	0.0000	1.0000
K2P	36	-2150.9427	4373.8854	0.0000	1.0000
SYM	40	-2147.0400	4374.0801	0.0000	1.0000
JC69I	36	-2151.4902	4374.9804	0.0000	1.0000
F81	38	-2158.7965	4393.5929	0.0000	1.0000
JC69	35	-2175.9417	4421.8835	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2101.1255	4468.1066	0.7095	0.7095
HKYI	40	-2102.0652	4469.9861	0.2772	0.9867
GTRG	44	-2092.3885	4477.2182	0.0075	0.9942
HKYIG	41	-2103.2503	4479.0026	0.0031	0.9972
GTRI	44	-2093.4045	4479.2502	0.0027	0.9999
K2PG	37	-2120.7760	4487.4684	0.0000	1.0000
GTRIG	45	-2094.4671	4488.0218	0.0000	1.0000
K2PI	37	-2124.5099	4494.9362	0.0000	1.0000
K2PIG	38	-2122.8022	4498.1672	0.0000	1.0000
SYMG	41	-2116.6103	4505.7227	0.0000	1.0000
SYMIG	42	-2116.2866	4511.7216	0.0000	1.0000
SYMI	41	-2120.5225	4513.5470	0.0000	1.0000
F81G	39	-2129.6285	4518.4663	0.0000	1.0000
F81I	39	-2130.5230	4520.2552	0.0000	1.0000
HKY	39	-2132.2179	4523.6450	0.0000	1.0000
F81IG	40	-2129.3587	4524.5730	0.0000	1.0000
JC69G	36	-2147.1946	4533.6592	0.0000	1.0000
GTR	43	-2125.4517	4536.6982	0.0000	1.0000
JC69IG	37	-2146.9225	4539.7614	0.0000	1.0000
K2P	36	-2150.9427	4541.1555	0.0000	1.0000
JC69I	36	-2151.4902	4542.2504	0.0000	1.0000
SYM	40	-2147.0400	4559.9357	0.0000	1.0000
F81	38	-2158.7965	4570.1558	0.0000	1.0000
JC69	35	-2175.9417	4584.5071	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/chr1_32334.phylip = 1 - 770;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32334.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/chr1_32334.phylip = 1 - 770;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32334.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/chr1_32334.phylip = 1 - 770;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32334.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

