
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:01 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_3158.phylip" (19 taxa, 413 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
Minimum BIC  model: HKYIG


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
HKYIG	41	-1499.0683	3089.4197	0.9318	0.9318
GTRIG	45	-1496.9933	3095.2673	0.0501	0.9818
HKYG	40	-1504.4437	3097.7046	0.0148	0.9966
HKYI	40	-1506.1521	3101.1214	0.0027	0.9993
GTRG	44	-1502.6455	3104.0518	0.0006	0.9999
GTRI	44	-1505.0673	3108.8955	0.0001	1.0000
K2PIG	38	-1523.8084	3131.5420	0.0000	1.0000
K2PI	37	-1526.5697	3134.6381	0.0000	1.0000
SYMIG	42	-1521.4899	3136.7421	0.0000	1.0000
K2PG	37	-1530.4244	3142.3474	0.0000	1.0000
SYMG	41	-1527.2162	3145.7155	0.0000	1.0000
SYMI	41	-1528.8856	3149.0541	0.0000	1.0000
HKY	39	-1532.7252	3151.8150	0.0000	1.0000
F81IG	40	-1533.0332	3154.8837	0.0000	1.0000
F81G	39	-1535.5273	3157.4191	0.0000	1.0000
GTR	43	-1531.0972	3158.4492	0.0000	1.0000
F81I	39	-1536.3335	3159.0316	0.0000	1.0000
JC69IG	37	-1557.2235	3195.9457	0.0000	1.0000
JC69I	36	-1559.1750	3197.4351	0.0000	1.0000
JC69G	36	-1559.3410	3197.7670	0.0000	1.0000
K2P	36	-1560.6559	3200.3969	0.0000	1.0000
SYM	40	-1557.9878	3204.7927	0.0000	1.0000
F81	38	-1563.7376	3211.4004	0.0000	1.0000
JC69	35	-1588.6743	3254.0330	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1499.0683	3080.1366	0.8604	0.8604
GTRIG	45	-1496.9933	3083.9867	0.1255	0.9859
HKYG	40	-1504.4437	3088.8874	0.0108	0.9967
HKYI	40	-1506.1521	3092.3042	0.0020	0.9987
GTRG	44	-1502.6455	3093.2909	0.0012	0.9999
GTRI	44	-1505.0673	3098.1346	0.0001	1.0000
K2PIG	38	-1523.8084	3123.6168	0.0000	1.0000
SYMIG	42	-1521.4899	3126.9799	0.0000	1.0000
K2PI	37	-1526.5697	3127.1395	0.0000	1.0000
K2PG	37	-1530.4244	3134.8487	0.0000	1.0000
SYMG	41	-1527.2162	3136.4325	0.0000	1.0000
SYMI	41	-1528.8856	3139.7711	0.0000	1.0000
HKY	39	-1532.7252	3143.4503	0.0000	1.0000
F81IG	40	-1533.0332	3146.0665	0.0000	1.0000
GTR	43	-1531.0972	3148.1944	0.0000	1.0000
F81G	39	-1535.5273	3149.0545	0.0000	1.0000
F81I	39	-1536.3335	3150.6670	0.0000	1.0000
JC69IG	37	-1557.2235	3188.4470	0.0000	1.0000
JC69I	36	-1559.1750	3190.3500	0.0000	1.0000
JC69G	36	-1559.3410	3190.6819	0.0000	1.0000
K2P	36	-1560.6559	3193.3118	0.0000	1.0000
SYM	40	-1557.9878	3195.9755	0.0000	1.0000
F81	38	-1563.7376	3203.4752	0.0000	1.0000
JC69	35	-1588.6743	3247.3486	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYIG	41	-1499.0683	3245.0980	0.9000	0.9000
HKYG	40	-1504.4437	3249.8253	0.0847	0.9846
HKYI	40	-1506.1521	3253.2421	0.0153	1.0000
GTRIG	45	-1496.9933	3265.0418	0.0000	1.0000
GTRG	44	-1502.6455	3270.3226	0.0000	1.0000
GTRI	44	-1505.0673	3275.1663	0.0000	1.0000
K2PI	37	-1526.5697	3276.0070	0.0000	1.0000
K2PIG	38	-1523.8084	3276.5078	0.0000	1.0000
K2PG	37	-1530.4244	3283.7163	0.0000	1.0000
SYMIG	42	-1521.4899	3295.9647	0.0000	1.0000
HKY	39	-1532.7252	3300.3648	0.0000	1.0000
SYMG	41	-1527.2162	3301.3939	0.0000	1.0000
SYMI	41	-1528.8856	3304.7325	0.0000	1.0000
F81G	39	-1535.5273	3305.9690	0.0000	1.0000
F81IG	40	-1533.0332	3307.0044	0.0000	1.0000
F81I	39	-1536.3335	3307.5815	0.0000	1.0000
GTR	43	-1531.0972	3321.2027	0.0000	1.0000
JC69I	36	-1559.1750	3335.1941	0.0000	1.0000
JC69G	36	-1559.3410	3335.5261	0.0000	1.0000
JC69IG	37	-1557.2235	3337.3146	0.0000	1.0000
K2P	36	-1560.6559	3338.1559	0.0000	1.0000
F81	38	-1563.7376	3356.3662	0.0000	1.0000
SYM	40	-1557.9878	3356.9134	0.0000	1.0000
JC69	35	-1588.6743	3388.1693	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3158.phylip = 1 - 413;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3158.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3158.phylip = 1 - 413;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3158.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3158.phylip = 1 - 413;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_3158.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

