
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:15 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/chr3_23229.phylip" (19 taxa, 490 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	-1365.3151	2827.5291	0.5504	0.5504
GTRG	44	-1365.7828	2828.4644	0.3448	0.8953
GTRIG	45	-1365.7824	2830.8891	0.1026	0.9979
HKYI	40	-1376.7647	2840.8345	0.0007	0.9986
HKYG	40	-1376.7729	2840.8509	0.0007	0.9993
SYMI	41	-1376.5006	2842.6887	0.0003	0.9995
HKYIG	41	-1376.7726	2843.2328	0.0002	0.9998
SYMG	41	-1376.9342	2843.5558	0.0002	0.9999
SYMIG	42	-1376.9339	2845.9484	0.0001	1.0000
K2PG	37	-1387.2957	2854.8126	0.0000	1.0000
K2PI	37	-1387.3375	2854.8963	0.0000	1.0000
K2PIG	38	-1387.3011	2857.1743	0.0000	1.0000
GTR	43	-1383.6989	2861.8821	0.0000	1.0000
SYM	40	-1393.3888	2874.0827	0.0000	1.0000
HKY	39	-1397.6051	2880.1436	0.0000	1.0000
F81G	39	-1400.5539	2886.0411	0.0000	1.0000
F81I	39	-1400.8582	2886.6496	0.0000	1.0000
F81IG	40	-1400.5410	2888.3871	0.0000	1.0000
K2P	36	-1407.0853	2892.0514	0.0000	1.0000
JC69G	36	-1408.6735	2895.2279	0.0000	1.0000
JC69I	36	-1408.9750	2895.8309	0.0000	1.0000
JC69IG	37	-1408.6640	2897.5492	0.0000	1.0000
F81	38	-1418.9404	2920.4528	0.0000	1.0000
JC69	35	-1427.1210	2929.7927	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1365.3151	2818.6302	0.5379	0.5379
GTRG	44	-1365.7828	2819.5655	0.3370	0.8750
GTRIG	45	-1365.7824	2821.5648	0.1240	0.9990
HKYI	40	-1376.7647	2833.5294	0.0003	0.9993
HKYG	40	-1376.7729	2833.5457	0.0003	0.9996
SYMI	41	-1376.5006	2835.0012	0.0001	0.9998
HKYIG	41	-1376.7726	2835.5453	0.0001	0.9999
SYMG	41	-1376.9342	2835.8683	0.0001	1.0000
SYMIG	42	-1376.9339	2837.8678	0.0000	1.0000
K2PG	37	-1387.2957	2848.5913	0.0000	1.0000
K2PI	37	-1387.3375	2848.6751	0.0000	1.0000
K2PIG	38	-1387.3011	2850.6023	0.0000	1.0000
GTR	43	-1383.6989	2853.3978	0.0000	1.0000
SYM	40	-1393.3888	2866.7776	0.0000	1.0000
HKY	39	-1397.6051	2873.2102	0.0000	1.0000
F81G	39	-1400.5539	2879.1078	0.0000	1.0000
F81I	39	-1400.8582	2879.7163	0.0000	1.0000
F81IG	40	-1400.5410	2881.0819	0.0000	1.0000
K2P	36	-1407.0853	2886.1706	0.0000	1.0000
JC69G	36	-1408.6735	2889.3471	0.0000	1.0000
JC69I	36	-1408.9750	2889.9501	0.0000	1.0000
JC69IG	37	-1408.6640	2891.3279	0.0000	1.0000
F81	38	-1418.9404	2913.8807	0.0000	1.0000
JC69	35	-1427.1210	2924.2420	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1376.7647	3001.3056	0.2974	0.2974
HKYG	40	-1376.7729	3001.3220	0.2950	0.5924
GTRI	44	-1365.3151	3003.1841	0.1163	0.7086
K2PG	37	-1387.2957	3003.7843	0.0861	0.7947
K2PI	37	-1387.3375	3003.8681	0.0826	0.8773
GTRG	44	-1365.7828	3004.1193	0.0728	0.9502
SYMI	41	-1376.5006	3006.9718	0.0175	0.9677
HKYIG	41	-1376.7726	3007.5159	0.0133	0.9810
SYMG	41	-1376.9342	3007.8390	0.0113	0.9923
K2PIG	38	-1387.3011	3009.9897	0.0039	0.9962
GTRIG	45	-1365.7824	3010.3130	0.0033	0.9995
SYMIG	42	-1376.9339	3014.0328	0.0005	1.0000
GTR	43	-1383.6989	3033.7573	0.0000	1.0000
SYM	40	-1393.3888	3034.5538	0.0000	1.0000
HKY	39	-1397.6051	3036.7920	0.0000	1.0000
K2P	36	-1407.0853	3037.1692	0.0000	1.0000
JC69G	36	-1408.6735	3040.3457	0.0000	1.0000
JC69I	36	-1408.9750	3040.9487	0.0000	1.0000
F81G	39	-1400.5539	3042.6896	0.0000	1.0000
F81I	39	-1400.8582	3043.2981	0.0000	1.0000
JC69IG	37	-1408.6640	3046.5209	0.0000	1.0000
F81IG	40	-1400.5410	3048.8582	0.0000	1.0000
JC69	35	-1427.1210	3071.0462	0.0000	1.0000
F81	38	-1418.9404	3073.2681	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/chr3_23229.phylip = 1 - 490;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_23229.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/chr3_23229.phylip = 1 - 490;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_23229.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/chr3_23229.phylip = 1 - 490;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_23229.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

