
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:48 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/chr6_4410.phylip" (19 taxa, 473 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-1485.9252	3071.5460	0.7327	0.7327
GTRG	44	-1488.1956	3073.6435	0.2567	0.9894
HKYIG	41	-1495.3406	3080.6719	0.0076	0.9971
HKYG	40	-1497.9010	3083.3946	0.0020	0.9990
GTRI	44	-1493.9851	3085.2224	0.0008	0.9998
SYMIG	42	-1498.1624	3088.7248	0.0001	0.9999
SYMG	41	-1500.4477	3090.8861	0.0000	1.0000
HKYI	40	-1503.6138	3094.8201	0.0000	1.0000
K2PIG	38	-1508.6336	3100.0966	0.0000	1.0000
SYMI	41	-1505.5882	3101.1671	0.0000	1.0000
K2PG	37	-1511.1015	3102.6674	0.0000	1.0000
K2PI	37	-1516.1754	3112.8152	0.0000	1.0000
F81IG	40	-1525.6361	3138.8647	0.0000	1.0000
F81G	39	-1528.4801	3142.1658	0.0000	1.0000
F81I	39	-1533.7714	3152.7483	0.0000	1.0000
JC69IG	37	-1536.5771	3153.6185	0.0000	1.0000
JC69G	36	-1539.3768	3156.8637	0.0000	1.0000
JC69I	36	-1544.4238	3166.9578	0.0000	1.0000
GTR	43	-1539.3154	3173.4513	0.0000	1.0000
HKY	39	-1549.3289	3183.8632	0.0000	1.0000
SYM	40	-1551.5801	3190.7528	0.0000	1.0000
K2P	36	-1562.2171	3202.5444	0.0000	1.0000
F81	38	-1578.9036	3240.6368	0.0000	1.0000
JC69	35	-1589.9582	3255.6830	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1485.9252	3061.8505	0.7769	0.7769
GTRG	44	-1488.1956	3064.3912	0.2181	0.9951
HKYIG	41	-1495.3406	3072.6812	0.0035	0.9985
HKYG	40	-1497.9010	3075.8020	0.0007	0.9992
GTRI	44	-1493.9851	3075.9701	0.0007	0.9999
SYMIG	42	-1498.1624	3080.3248	0.0001	1.0000
SYMG	41	-1500.4477	3082.8954	0.0000	1.0000
HKYI	40	-1503.6138	3087.2275	0.0000	1.0000
SYMI	41	-1505.5882	3093.1764	0.0000	1.0000
K2PIG	38	-1508.6336	3093.2671	0.0000	1.0000
K2PG	37	-1511.1015	3096.2030	0.0000	1.0000
K2PI	37	-1516.1754	3106.3509	0.0000	1.0000
F81IG	40	-1525.6361	3131.2721	0.0000	1.0000
F81G	39	-1528.4801	3134.9602	0.0000	1.0000
F81I	39	-1533.7714	3145.5428	0.0000	1.0000
JC69IG	37	-1536.5771	3147.1542	0.0000	1.0000
JC69G	36	-1539.3768	3150.7536	0.0000	1.0000
JC69I	36	-1544.4238	3160.8477	0.0000	1.0000
GTR	43	-1539.3154	3164.6308	0.0000	1.0000
HKY	39	-1549.3289	3176.6577	0.0000	1.0000
SYM	40	-1551.5801	3183.1602	0.0000	1.0000
K2P	36	-1562.2171	3196.4343	0.0000	1.0000
F81	38	-1578.9036	3233.8073	0.0000	1.0000
JC69	35	-1589.9582	3249.9164	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1497.9010	3242.1658	0.5750	0.5750
HKYIG	41	-1495.3406	3243.2041	0.3421	0.9171
GTRG	44	-1488.1956	3247.3914	0.0422	0.9592
GTRIG	45	-1485.9252	3249.0098	0.0188	0.9780
K2PG	37	-1511.1015	3250.0895	0.0109	0.9889
K2PIG	38	-1508.6336	3251.3127	0.0059	0.9949
SYMG	41	-1500.4477	3253.4183	0.0021	0.9970
HKYI	40	-1503.6138	3253.5913	0.0019	0.9989
SYMIG	42	-1498.1624	3255.0068	0.0009	0.9998
GTRI	44	-1493.9851	3258.9703	0.0001	0.9999
K2PI	37	-1516.1754	3260.2374	0.0001	1.0000
SYMI	41	-1505.5882	3263.6993	0.0000	1.0000
F81G	39	-1528.4801	3297.1650	0.0000	1.0000
F81IG	40	-1525.6361	3297.6359	0.0000	1.0000
JC69G	36	-1539.3768	3300.4811	0.0000	1.0000
JC69IG	37	-1536.5771	3301.0407	0.0000	1.0000
F81I	39	-1533.7714	3307.7475	0.0000	1.0000
JC69I	36	-1544.4238	3310.5751	0.0000	1.0000
HKY	39	-1549.3289	3338.8624	0.0000	1.0000
GTR	43	-1539.3154	3343.4719	0.0000	1.0000
K2P	36	-1562.2171	3346.1617	0.0000	1.0000
SYM	40	-1551.5801	3349.5241	0.0000	1.0000
F81	38	-1578.9036	3391.8529	0.0000	1.0000
JC69	35	-1589.9582	3395.4848	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4410.phylip = 1 - 473;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4410.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4410.phylip = 1 - 473;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4410.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr6_4410.phylip = 1 - 473;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_4410.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

