
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:08 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_5583.phylip" (19 taxa, 243 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
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
GTRI	44	-692.0794	1492.1589	0.3430	0.3430
GTRG	44	-692.2510	1492.5020	0.2889	0.6318
HKYG	40	-698.8637	1493.9650	0.1390	0.7709
HKYI	40	-698.9241	1494.0858	0.1309	0.9017
GTRIG	45	-692.2512	1495.5175	0.0640	0.9657
HKYIG	41	-698.8754	1496.8852	0.0323	0.9980
K2PG	37	-708.2157	1504.1486	0.0009	0.9988
K2PI	37	-708.3780	1504.4731	0.0007	0.9995
K2PIG	38	-708.1708	1506.8710	0.0002	0.9998
SYMG	41	-704.5635	1508.2613	0.0001	0.9999
SYMI	41	-704.6235	1508.3813	0.0001	1.0000
SYMIG	42	-704.5748	1511.2095	0.0000	1.0000
HKY	39	-710.2862	1513.9418	0.0000	1.0000
GTR	43	-704.6868	1514.3887	0.0000	1.0000
K2P	36	-719.7532	1524.4384	0.0000	1.0000
SYM	40	-715.2079	1526.6534	0.0000	1.0000
F81G	39	-722.5854	1538.5403	0.0000	1.0000
F81I	39	-722.6090	1538.5874	0.0000	1.0000
F81IG	40	-722.6097	1541.4569	0.0000	1.0000
JC69G	36	-730.5214	1545.9748	0.0000	1.0000
JC69I	36	-730.5744	1546.0809	0.0000	1.0000
JC69IG	37	-730.5309	1548.7788	0.0000	1.0000
F81	38	-733.6468	1557.8231	0.0000	1.0000
JC69	35	-741.4572	1565.0883	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-692.0794	1472.1589	0.4357	0.4357
GTRG	44	-692.2510	1472.5020	0.3670	0.8028
GTRIG	45	-692.2512	1474.5023	0.1350	0.9378
HKYG	40	-698.8637	1477.7274	0.0269	0.9647
HKYI	40	-698.9241	1477.8482	0.0253	0.9900
HKYIG	41	-698.8754	1479.7509	0.0098	0.9998
K2PG	37	-708.2157	1490.4315	0.0000	0.9999
K2PI	37	-708.3780	1490.7560	0.0000	0.9999
SYMG	41	-704.5635	1491.1270	0.0000	0.9999
SYMI	41	-704.6235	1491.2470	0.0000	1.0000
K2PIG	38	-708.1708	1492.3415	0.0000	1.0000
SYMIG	42	-704.5748	1493.1495	0.0000	1.0000
GTR	43	-704.6868	1495.3736	0.0000	1.0000
HKY	39	-710.2862	1498.5724	0.0000	1.0000
SYM	40	-715.2079	1510.4158	0.0000	1.0000
K2P	36	-719.7532	1511.5064	0.0000	1.0000
F81G	39	-722.5854	1523.1708	0.0000	1.0000
F81I	39	-722.6090	1523.2179	0.0000	1.0000
F81IG	40	-722.6097	1525.2193	0.0000	1.0000
JC69G	36	-730.5214	1533.0427	0.0000	1.0000
JC69I	36	-730.5744	1533.1489	0.0000	1.0000
JC69IG	37	-730.5309	1535.0617	0.0000	1.0000
F81	38	-733.6468	1543.2936	0.0000	1.0000
JC69	35	-741.4572	1552.9144	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-698.8637	1617.4498	0.3754	0.3754
HKYI	40	-698.9241	1617.5707	0.3534	0.7287
K2PG	37	-708.2157	1619.6748	0.1234	0.8521
K2PI	37	-708.3780	1619.9993	0.1049	0.9570
HKYIG	41	-698.8754	1622.9664	0.0238	0.9808
K2PIG	38	-708.1708	1625.0779	0.0083	0.9891
GTRI	44	-692.0794	1625.8536	0.0056	0.9947
GTRG	44	-692.2510	1626.1967	0.0047	0.9995
GTRIG	45	-692.2512	1631.6901	0.0003	0.9998
SYMG	41	-704.5635	1634.3425	0.0001	0.9998
SYMI	41	-704.6235	1634.4625	0.0001	0.9999
HKY	39	-710.2862	1634.8018	0.0001	1.0000
K2P	36	-719.7532	1637.2566	0.0000	1.0000
SYMIG	42	-704.5748	1639.8581	0.0000	1.0000
GTR	43	-704.6868	1645.5753	0.0000	1.0000
SYM	40	-715.2079	1650.1382	0.0000	1.0000
JC69G	36	-730.5214	1658.7929	0.0000	1.0000
JC69I	36	-730.5744	1658.8991	0.0000	1.0000
F81G	39	-722.5854	1659.4002	0.0000	1.0000
F81I	39	-722.6090	1659.4473	0.0000	1.0000
JC69IG	37	-730.5309	1664.3050	0.0000	1.0000
F81IG	40	-722.6097	1664.9418	0.0000	1.0000
JC69	35	-741.4572	1675.1715	0.0000	1.0000
F81	38	-733.6468	1676.0300	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_5583.phylip = 1 - 243;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5583.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_5583.phylip = 1 - 243;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5583.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5583.phylip = 1 - 243;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5583.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

