
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:18 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_28903.phylip" (19 taxa, 478 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
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
HKYI	40	-1402.8609	2893.2274	0.3654	0.3654
HKYG	40	-1403.2000	2893.9057	0.2603	0.6258
GTRI	44	-1398.8674	2894.8803	0.1599	0.7857
GTRG	44	-1399.2916	2895.7287	0.1046	0.8903
HKYIG	41	-1403.1997	2896.2984	0.0787	0.9690
GTRIG	45	-1399.2913	2898.1659	0.0309	1.0000
HKY	39	-1413.7035	2912.5303	0.0000	1.0000
K2PI	37	-1417.1551	2914.7011	0.0000	1.0000
K2PG	37	-1417.2452	2914.8812	0.0000	1.0000
GTR	43	-1410.5683	2915.8556	0.0000	1.0000
K2PIG	38	-1417.2596	2917.2708	0.0000	1.0000
SYMI	41	-1415.5099	2920.9189	0.0000	1.0000
SYMG	41	-1415.6381	2921.1752	0.0000	1.0000
SYMIG	42	-1415.6563	2923.6161	0.0000	1.0000
K2P	36	-1427.5900	2933.2209	0.0000	1.0000
SYM	40	-1425.9332	2939.3721	0.0000	1.0000
F81I	39	-1444.1451	2973.4135	0.0000	1.0000
F81G	39	-1444.3450	2973.8132	0.0000	1.0000
F81IG	40	-1444.3446	2976.1950	0.0000	1.0000
JC69I	36	-1455.3522	2988.7452	0.0000	1.0000
JC69G	36	-1455.5189	2989.0786	0.0000	1.0000
F81	38	-1453.6353	2990.0222	0.0000	1.0000
JC69IG	37	-1455.5186	2991.4280	0.0000	1.0000
JC69	35	-1464.9789	3005.6592	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1402.8609	2885.7217	0.2592	0.2592
GTRI	44	-1398.8674	2885.7348	0.2576	0.5168
HKYG	40	-1403.2000	2886.4000	0.1847	0.7015
GTRG	44	-1399.2916	2886.5832	0.1685	0.8700
HKYIG	41	-1403.1997	2888.3994	0.0680	0.9380
GTRIG	45	-1399.2913	2888.5826	0.0620	1.0000
HKY	39	-1413.7035	2905.4071	0.0000	1.0000
GTR	43	-1410.5683	2907.1367	0.0000	1.0000
K2PI	37	-1417.1551	2908.3102	0.0000	1.0000
K2PG	37	-1417.2452	2908.4903	0.0000	1.0000
K2PIG	38	-1417.2596	2910.5191	0.0000	1.0000
SYMI	41	-1415.5099	2913.0198	0.0000	1.0000
SYMG	41	-1415.6381	2913.2761	0.0000	1.0000
SYMIG	42	-1415.6563	2915.3126	0.0000	1.0000
K2P	36	-1427.5900	2927.1801	0.0000	1.0000
SYM	40	-1425.9332	2931.8663	0.0000	1.0000
F81I	39	-1444.1451	2966.2902	0.0000	1.0000
F81G	39	-1444.3450	2966.6899	0.0000	1.0000
F81IG	40	-1444.3446	2968.6892	0.0000	1.0000
JC69I	36	-1455.3522	2982.7044	0.0000	1.0000
JC69G	36	-1455.5189	2983.0378	0.0000	1.0000
F81	38	-1453.6353	2983.2705	0.0000	1.0000
JC69IG	37	-1455.5186	2985.0371	0.0000	1.0000
JC69	35	-1464.9789	2999.9578	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1402.8609	3052.5061	0.5687	0.5687
HKYG	40	-1403.2000	3053.1844	0.4051	0.9738
HKYIG	41	-1403.1997	3059.3534	0.0185	0.9923
K2PI	37	-1417.1551	3062.5858	0.0037	0.9960
K2PG	37	-1417.2452	3062.7659	0.0034	0.9994
HKY	39	-1413.7035	3068.0219	0.0002	0.9996
K2PIG	38	-1417.2596	3068.9643	0.0002	0.9998
GTRI	44	-1398.8674	3069.1977	0.0001	0.9999
GTRG	44	-1399.2916	3070.0460	0.0001	1.0000
GTRIG	45	-1399.2913	3076.2150	0.0000	1.0000
K2P	36	-1427.5900	3077.2861	0.0000	1.0000
SYMI	41	-1415.5099	3083.9739	0.0000	1.0000
SYMG	41	-1415.6381	3084.2302	0.0000	1.0000
GTR	43	-1410.5683	3086.4299	0.0000	1.0000
SYMIG	42	-1415.6563	3090.4363	0.0000	1.0000
SYM	40	-1425.9332	3098.6508	0.0000	1.0000
F81I	39	-1444.1451	3128.9050	0.0000	1.0000
F81G	39	-1444.3450	3129.3047	0.0000	1.0000
JC69I	36	-1455.3522	3132.8103	0.0000	1.0000
JC69G	36	-1455.5189	3133.1438	0.0000	1.0000
F81IG	40	-1444.3446	3135.4737	0.0000	1.0000
JC69IG	37	-1455.5186	3139.3127	0.0000	1.0000
F81	38	-1453.6353	3141.7157	0.0000	1.0000
JC69	35	-1464.9789	3145.8942	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28903.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28903.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;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28903.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28903.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;


[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_28903.phylip = 1 - 478;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28903.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

