
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:21 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_14899.phylip" (19 taxa, 690 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	-1475.7732	3045.6860	0.3443	0.3443
GTRG	44	-1475.8295	3045.7986	0.3254	0.6697
GTRIG	45	-1475.8292	3048.0869	0.1036	0.7733
HKYI	40	-1481.5582	3048.1703	0.0994	0.8727
HKYG	40	-1481.5975	3048.2489	0.0956	0.9683
HKYIG	41	-1481.5987	3050.5122	0.0308	0.9991
GTR	43	-1483.2689	3058.3954	0.0006	0.9997
HKY	39	-1488.5934	3059.9869	0.0003	1.0000
F81I	39	-1501.2726	3085.3452	0.0000	1.0000
F81G	39	-1501.3124	3085.4248	0.0000	1.0000
F81IG	40	-1501.3153	3087.6846	0.0000	1.0000
F81	38	-1507.9438	3096.4406	0.0000	1.0000
K2PI	37	-1515.0338	3108.3804	0.0000	1.0000
K2PG	37	-1515.0693	3108.4516	0.0000	1.0000
K2PIG	38	-1515.0768	3110.7066	0.0000	1.0000
SYMI	41	-1512.1467	3111.6081	0.0000	1.0000
SYMG	41	-1512.2162	3111.7471	0.0000	1.0000
SYMIG	42	-1512.2159	3114.0144	0.0000	1.0000
K2P	36	-1521.7967	3119.6730	0.0000	1.0000
SYM	40	-1518.7739	3122.6016	0.0000	1.0000
JC69I	36	-1531.9358	3139.9513	0.0000	1.0000
JC69G	36	-1531.9724	3140.0245	0.0000	1.0000
JC69IG	37	-1531.9784	3142.2696	0.0000	1.0000
JC69	35	-1538.5374	3150.9279	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1475.7732	3039.5464	0.3727	0.3727
GTRG	44	-1475.8295	3039.6591	0.3522	0.7249
GTRIG	45	-1475.8292	3041.6583	0.1296	0.8545
HKYI	40	-1481.5582	3043.1164	0.0625	0.9171
HKYG	40	-1481.5975	3043.1949	0.0601	0.9772
HKYIG	41	-1481.5987	3045.1974	0.0221	0.9993
GTR	43	-1483.2689	3052.5378	0.0006	0.9999
HKY	39	-1488.5934	3055.1869	0.0001	1.0000
F81I	39	-1501.2726	3080.5452	0.0000	1.0000
F81G	39	-1501.3124	3080.6248	0.0000	1.0000
F81IG	40	-1501.3153	3082.6307	0.0000	1.0000
F81	38	-1507.9438	3091.8876	0.0000	1.0000
K2PI	37	-1515.0338	3104.0676	0.0000	1.0000
K2PG	37	-1515.0693	3104.1387	0.0000	1.0000
K2PIG	38	-1515.0768	3106.1536	0.0000	1.0000
SYMI	41	-1512.1467	3106.2933	0.0000	1.0000
SYMG	41	-1512.2162	3106.4323	0.0000	1.0000
SYMIG	42	-1512.2159	3108.4318	0.0000	1.0000
K2P	36	-1521.7967	3115.5933	0.0000	1.0000
SYM	40	-1518.7739	3117.5477	0.0000	1.0000
JC69I	36	-1531.9358	3135.8716	0.0000	1.0000
JC69G	36	-1531.9724	3135.9448	0.0000	1.0000
JC69IG	37	-1531.9784	3137.9567	0.0000	1.0000
JC69	35	-1538.5374	3147.0747	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1481.5582	3224.5841	0.4944	0.4944
HKYG	40	-1481.5975	3224.6626	0.4754	0.9698
HKYIG	41	-1481.5987	3231.2017	0.0181	0.9879
HKY	39	-1488.5934	3232.1178	0.0114	0.9993
GTRI	44	-1475.7732	3239.1609	0.0003	0.9997
GTRG	44	-1475.8295	3239.2735	0.0003	1.0000
GTRIG	45	-1475.8292	3245.8094	0.0000	1.0000
GTR	43	-1483.2689	3247.6156	0.0000	1.0000
F81I	39	-1501.2726	3257.4762	0.0000	1.0000
F81G	39	-1501.3124	3257.5558	0.0000	1.0000
F81IG	40	-1501.3153	3264.0983	0.0000	1.0000
F81	38	-1507.9438	3264.2818	0.0000	1.0000
K2PI	37	-1515.0338	3271.9251	0.0000	1.0000
K2PG	37	-1515.0693	3271.9963	0.0000	1.0000
K2PIG	38	-1515.0768	3278.5479	0.0000	1.0000
K2P	36	-1521.7967	3278.9142	0.0000	1.0000
SYMI	41	-1512.1467	3292.2977	0.0000	1.0000
SYMG	41	-1512.2162	3292.4367	0.0000	1.0000
SYMIG	42	-1512.2159	3298.9728	0.0000	1.0000
SYM	40	-1518.7739	3299.0154	0.0000	1.0000
JC69I	36	-1531.9358	3299.1925	0.0000	1.0000
JC69G	36	-1531.9724	3299.2657	0.0000	1.0000
JC69IG	37	-1531.9784	3305.8143	0.0000	1.0000
JC69	35	-1538.5374	3305.8589	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/chr1_14899.phylip = 1 - 690;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14899.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/chr1_14899.phylip = 1 - 690;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14899.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/chr1_14899.phylip = 1 - 690;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_14899.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

