
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:10 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_5768.phylip" (19 taxa, 263 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: K2PI


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	-738.5158	1571.8064	0.3919	0.3919
HKYG	40	-738.6153	1572.0053	0.3548	0.7466
HKYIG	41	-738.6151	1574.8138	0.0871	0.8338
K2PI	37	-744.4020	1575.3017	0.0683	0.9020
K2PG	37	-744.5278	1575.5534	0.0602	0.9622
K2PIG	38	-744.5277	1578.2875	0.0153	0.9775
GTRI	44	-736.4796	1579.1243	0.0101	0.9876
GTRG	44	-736.6177	1579.4005	0.0088	0.9964
GTRIG	45	-736.6176	1582.3135	0.0020	0.9985
SYMI	41	-743.4049	1584.3936	0.0007	0.9992
SYMG	41	-743.5513	1584.6863	0.0006	0.9998
SYMIG	42	-743.5513	1587.5208	0.0002	1.0000
HKY	39	-749.7692	1591.5295	0.0000	1.0000
F81I	39	-751.7922	1595.5754	0.0000	1.0000
F81G	39	-751.9258	1595.8427	0.0000	1.0000
K2P	36	-756.1467	1596.0811	0.0000	1.0000
GTR	43	-747.0242	1597.3269	0.0000	1.0000
JC69I	36	-757.2311	1598.2497	0.0000	1.0000
JC69G	36	-757.3891	1598.5658	0.0000	1.0000
F81IG	40	-751.9258	1598.6264	0.0000	1.0000
JC69IG	37	-757.3890	1601.2758	0.0000	1.0000
SYM	40	-754.6288	1604.0324	0.0000	1.0000
F81	38	-762.6883	1614.6087	0.0000	1.0000
JC69	35	-768.4483	1617.9978	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-738.5158	1557.0316	0.3738	0.3738
HKYG	40	-738.6153	1557.2305	0.3384	0.7122
HKYIG	41	-738.6151	1559.2301	0.1245	0.8368
GTRI	44	-736.4796	1560.9592	0.0525	0.8892
GTRG	44	-736.6177	1561.2354	0.0457	0.9349
K2PI	37	-744.4020	1562.8040	0.0209	0.9558
K2PG	37	-744.5278	1563.0556	0.0184	0.9741
GTRIG	45	-736.6176	1563.2352	0.0168	0.9910
K2PIG	38	-744.5277	1565.0554	0.0068	0.9977
SYMI	41	-743.4049	1568.8099	0.0010	0.9988
SYMG	41	-743.5513	1569.1026	0.0009	0.9996
SYMIG	42	-743.5513	1571.1026	0.0003	1.0000
HKY	39	-749.7692	1577.5384	0.0000	1.0000
GTR	43	-747.0242	1580.0483	0.0000	1.0000
F81I	39	-751.7922	1581.5843	0.0000	1.0000
F81G	39	-751.9258	1581.8517	0.0000	1.0000
F81IG	40	-751.9258	1583.8516	0.0000	1.0000
K2P	36	-756.1467	1584.2935	0.0000	1.0000
JC69I	36	-757.2311	1586.4621	0.0000	1.0000
JC69G	36	-757.3891	1586.7781	0.0000	1.0000
JC69IG	37	-757.3890	1588.7781	0.0000	1.0000
SYM	40	-754.6288	1589.2576	0.0000	1.0000
F81	38	-762.6883	1601.3765	0.0000	1.0000
JC69	35	-768.4483	1606.8965	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-744.4020	1694.9737	0.4757	0.4757
K2PG	37	-744.5278	1695.2253	0.4195	0.8952
HKYI	40	-738.5158	1699.9178	0.0402	0.9354
HKYG	40	-738.6153	1700.1167	0.0364	0.9717
K2PIG	38	-744.5277	1700.7973	0.0259	0.9976
HKYIG	41	-738.6151	1705.6884	0.0022	0.9998
K2P	36	-756.1467	1712.8910	0.0001	0.9999
JC69I	36	-757.2311	1715.0597	0.0000	0.9999
SYMI	41	-743.4049	1715.2682	0.0000	0.9999
JC69G	36	-757.3891	1715.3757	0.0000	1.0000
SYMG	41	-743.5513	1715.5609	0.0000	1.0000
HKY	39	-749.7692	1716.8524	0.0000	1.0000
GTRI	44	-736.4796	1718.1340	0.0000	1.0000
GTRG	44	-736.6177	1718.4102	0.0000	1.0000
F81I	39	-751.7922	1720.8983	0.0000	1.0000
JC69IG	37	-757.3890	1720.9478	0.0000	1.0000
SYMIG	42	-743.5513	1721.1331	0.0000	1.0000
F81G	39	-751.9258	1721.1657	0.0000	1.0000
GTRIG	45	-736.6176	1723.9821	0.0000	1.0000
F81IG	40	-751.9258	1726.7378	0.0000	1.0000
JC69	35	-768.4483	1731.9219	0.0000	1.0000
SYM	40	-754.6288	1732.1438	0.0000	1.0000
GTR	43	-747.0242	1733.6510	0.0000	1.0000
F81	38	-762.6883	1737.1184	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/chr3_5768.phylip = 1 - 263;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5768.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/chr3_5768.phylip = 1 - 263;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5768.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 (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5768.phylip = 1 - 263;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5768.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


-------------------------------------------------------------
End of Output

