
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:38 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/chr2_22071.phylip" (19 taxa, 520 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	-1376.5500	2849.4368	0.3510	0.3510
GTRI	44	-1376.7204	2849.7775	0.2960	0.6471
GTRIG	45	-1376.3193	2851.3728	0.1333	0.7804
HKYG	40	-1382.5893	2852.0261	0.0962	0.8766
HKYI	40	-1382.7279	2852.3033	0.0837	0.9603
HKYIG	41	-1382.2993	2853.8036	0.0395	0.9999
K2PG	37	-1393.7628	2867.3597	0.0000	0.9999
K2PI	37	-1393.9352	2867.7044	0.0000	1.0000
K2PIG	38	-1393.1354	2868.4331	0.0000	1.0000
SYMG	41	-1390.7480	2870.7010	0.0000	1.0000
SYMI	41	-1390.9210	2871.0470	0.0000	1.0000
SYMIG	42	-1390.1286	2871.8295	0.0000	1.0000
F81G	39	-1404.0092	2892.5184	0.0000	1.0000
F81I	39	-1404.1849	2892.8699	0.0000	1.0000
F81IG	40	-1403.6342	2894.1161	0.0000	1.0000
GTR	43	-1401.7634	2897.4763	0.0000	1.0000
HKY	39	-1407.8273	2900.1546	0.0000	1.0000
JC69G	36	-1414.1689	2905.8533	0.0000	1.0000
JC69I	36	-1414.3505	2906.2165	0.0000	1.0000
JC69IG	37	-1413.7296	2907.2932	0.0000	1.0000
K2P	36	-1419.2627	2916.0409	0.0000	1.0000
SYM	40	-1415.7434	2918.3343	0.0000	1.0000
F81	38	-1428.4166	2938.9954	0.0000	1.0000
JC69	35	-1438.6997	2952.6061	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1376.5500	2841.1000	0.3825	0.3825
GTRI	44	-1376.7204	2841.4407	0.3226	0.7051
GTRIG	45	-1376.3193	2842.6386	0.1772	0.8824
HKYG	40	-1382.5893	2845.1785	0.0498	0.9321
HKYI	40	-1382.7279	2845.4557	0.0433	0.9755
HKYIG	41	-1382.2993	2846.5986	0.0245	1.0000
K2PG	37	-1393.7628	2861.5256	0.0000	1.0000
K2PI	37	-1393.9352	2861.8704	0.0000	1.0000
K2PIG	38	-1393.1354	2862.2709	0.0000	1.0000
SYMG	41	-1390.7480	2863.4960	0.0000	1.0000
SYMI	41	-1390.9210	2863.8420	0.0000	1.0000
SYMIG	42	-1390.1286	2864.2571	0.0000	1.0000
F81G	39	-1404.0092	2886.0184	0.0000	1.0000
F81I	39	-1404.1849	2886.3699	0.0000	1.0000
F81IG	40	-1403.6342	2887.2685	0.0000	1.0000
GTR	43	-1401.7634	2889.5268	0.0000	1.0000
HKY	39	-1407.8273	2893.6546	0.0000	1.0000
JC69G	36	-1414.1689	2900.3378	0.0000	1.0000
JC69I	36	-1414.3505	2900.7010	0.0000	1.0000
JC69IG	37	-1413.7296	2901.4591	0.0000	1.0000
K2P	36	-1419.2627	2910.5254	0.0000	1.0000
SYM	40	-1415.7434	2911.4867	0.0000	1.0000
F81	38	-1428.4166	2932.8332	0.0000	1.0000
JC69	35	-1438.6997	2947.3995	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1382.5893	3015.3317	0.4440	0.4440
HKYI	40	-1382.7279	3015.6089	0.3865	0.8305
K2PG	37	-1393.7628	3018.9173	0.0739	0.9044
K2PI	37	-1393.9352	3019.2621	0.0622	0.9666
HKYIG	41	-1382.2993	3021.0056	0.0260	0.9926
K2PIG	38	-1393.1354	3023.9164	0.0061	0.9987
GTRG	44	-1376.5500	3028.2684	0.0007	0.9994
GTRI	44	-1376.7204	3028.6092	0.0006	1.0000
GTRIG	45	-1376.3193	3034.0609	0.0000	1.0000
SYMG	41	-1390.7480	3037.9030	0.0000	1.0000
SYMI	41	-1390.9210	3038.2490	0.0000	1.0000
SYMIG	42	-1390.1286	3042.9180	0.0000	1.0000
F81G	39	-1404.0092	3051.9177	0.0000	1.0000
F81I	39	-1404.1849	3052.2692	0.0000	1.0000
JC69G	36	-1414.1689	3053.4756	0.0000	1.0000
JC69I	36	-1414.3505	3053.8388	0.0000	1.0000
F81IG	40	-1403.6342	3057.4216	0.0000	1.0000
JC69IG	37	-1413.7296	3058.8508	0.0000	1.0000
HKY	39	-1407.8273	3059.5540	0.0000	1.0000
K2P	36	-1419.2627	3063.6632	0.0000	1.0000
GTR	43	-1401.7634	3072.4414	0.0000	1.0000
SYM	40	-1415.7434	3081.6399	0.0000	1.0000
F81	38	-1428.4166	3094.4787	0.0000	1.0000
JC69	35	-1438.6997	3096.2835	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/chr2_22071.phylip = 1 - 520;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22071.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/chr2_22071.phylip = 1 - 520;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22071.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/chr2_22071.phylip = 1 - 520;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22071.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

