
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:11 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_10907.phylip" (19 taxa, 192 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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
HKYG	40	-684.9296	1471.5811	0.6355	0.6355
HKYIG	41	-684.8389	1474.6378	0.1378	0.7733
HKYI	40	-686.5257	1474.7732	0.1288	0.9021
K2PG	37	-691.9754	1476.2106	0.0628	0.9649
K2PIG	38	-691.6032	1478.5789	0.0192	0.9841
K2PI	37	-693.5123	1479.2843	0.0135	0.9976
GTRG	44	-684.8608	1484.6603	0.0009	0.9986
GTRI	44	-684.8691	1484.6769	0.0009	0.9995
SYMG	41	-691.3421	1487.6443	0.0002	0.9997
GTRIG	45	-684.8601	1488.0764	0.0002	0.9998
SYMI	41	-691.8673	1488.6946	0.0001	1.0000
SYMIG	42	-691.3167	1490.8750	0.0000	1.0000
HKY	39	-708.4430	1515.4123	0.0000	1.0000
K2P	36	-714.8958	1518.9788	0.0000	1.0000
GTR	43	-703.8870	1519.3416	0.0000	1.0000
SYM	40	-710.3175	1522.3569	0.0000	1.0000
F81G	39	-712.4141	1523.3546	0.0000	1.0000
F81I	39	-712.5065	1523.5394	0.0000	1.0000
F81IG	40	-712.4138	1526.5495	0.0000	1.0000
JC69I	36	-719.1211	1527.4293	0.0000	1.0000
JC69G	36	-719.3975	1527.9821	0.0000	1.0000
JC69IG	37	-719.3974	1531.0546	0.0000	1.0000
F81	38	-728.9341	1553.2408	0.0000	1.0000
JC69	35	-736.2276	1558.6091	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-684.9296	1449.8593	0.5940	0.5940
HKYIG	41	-684.8389	1451.6778	0.2393	0.8332
HKYI	40	-686.5257	1453.0514	0.1204	0.9536
GTRG	44	-684.8608	1457.7215	0.0117	0.9653
GTRI	44	-684.8691	1457.7381	0.0116	0.9768
K2PG	37	-691.9754	1457.9509	0.0104	0.9872
K2PIG	38	-691.6032	1459.2064	0.0055	0.9928
GTRIG	45	-684.8601	1459.7202	0.0043	0.9971
K2PI	37	-693.5123	1461.0245	0.0022	0.9993
SYMG	41	-691.3421	1464.6843	0.0004	0.9997
SYMI	41	-691.8673	1465.7346	0.0002	0.9999
SYMIG	42	-691.3167	1466.6333	0.0001	1.0000
GTR	43	-703.8870	1493.7741	0.0000	1.0000
HKY	39	-708.4430	1494.8860	0.0000	1.0000
SYM	40	-710.3175	1500.6350	0.0000	1.0000
K2P	36	-714.8958	1501.7917	0.0000	1.0000
F81G	39	-712.4141	1502.8282	0.0000	1.0000
F81I	39	-712.5065	1503.0131	0.0000	1.0000
F81IG	40	-712.4138	1504.8277	0.0000	1.0000
JC69I	36	-719.1211	1510.2422	0.0000	1.0000
JC69G	36	-719.3975	1510.7950	0.0000	1.0000
JC69IG	37	-719.3974	1512.7948	0.0000	1.0000
F81	38	-728.9341	1533.8682	0.0000	1.0000
JC69	35	-736.2276	1542.4553	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-691.9754	1578.4782	0.5339	0.5339
HKYG	40	-684.9296	1580.1591	0.2304	0.7643
K2PI	37	-693.5123	1581.5518	0.1148	0.8791
K2PIG	38	-691.6032	1582.9912	0.0559	0.9350
HKYI	40	-686.5257	1583.3512	0.0467	0.9817
HKYIG	41	-684.8389	1585.2352	0.0182	0.9999
SYMG	41	-691.3421	1598.2416	0.0000	1.0000
SYMI	41	-691.8673	1599.2919	0.0000	1.0000
GTRG	44	-684.8608	1601.0513	0.0000	1.0000
GTRI	44	-684.8691	1601.0679	0.0000	1.0000
SYMIG	42	-691.3167	1603.4481	0.0000	1.0000
GTRIG	45	-684.8601	1606.3075	0.0000	1.0000
K2P	36	-714.8958	1619.0615	0.0000	1.0000
HKY	39	-708.4430	1621.9283	0.0000	1.0000
JC69I	36	-719.1211	1627.5120	0.0000	1.0000
JC69G	36	-719.3975	1628.0649	0.0000	1.0000
F81G	39	-712.4141	1629.8706	0.0000	1.0000
F81I	39	-712.5065	1630.0554	0.0000	1.0000
SYM	40	-710.3175	1630.9348	0.0000	1.0000
JC69IG	37	-719.3974	1633.3222	0.0000	1.0000
GTR	43	-703.8870	1633.8464	0.0000	1.0000
F81IG	40	-712.4138	1635.1275	0.0000	1.0000
JC69	35	-736.2276	1656.4676	0.0000	1.0000
F81	38	-728.9341	1657.6531	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10907.phylip = 1 - 192;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10907.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10907.phylip = 1 - 192;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10907.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;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10907.phylip = 1 - 192;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_10907.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

