
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:44 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/chr2_25794.phylip" (19 taxa, 208 characters)

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


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	-665.7553	1431.1513	0.5046	0.5046
HKYIG	41	-664.5629	1431.8727	0.3518	0.8565
HKYG	40	-667.2409	1434.1225	0.1142	0.9707
K2PIG	38	-672.8678	1439.2740	0.0087	0.9794
K2PI	37	-674.5113	1439.5639	0.0075	0.9869
GTRI	44	-664.0077	1440.3098	0.0052	0.9921
GTRIG	45	-662.8206	1441.1968	0.0033	0.9954
SYMI	41	-670.0673	1442.8815	0.0014	0.9968
K2PG	37	-676.4603	1443.4619	0.0011	0.9979
SYMIG	42	-668.9211	1443.7330	0.0009	0.9988
GTRG	44	-665.7472	1443.7888	0.0009	0.9997
SYMG	41	-671.7972	1446.3415	0.0003	1.0000
F81G	39	-707.3907	1511.3528	0.0000	1.0000
F81I	39	-707.4382	1511.4479	0.0000	1.0000
F81IG	40	-707.2425	1514.1256	0.0000	1.0000
JC69G	36	-714.8139	1517.2068	0.0000	1.0000
JC69I	36	-714.8297	1517.2384	0.0000	1.0000
HKY	39	-710.9360	1518.4434	0.0000	1.0000
JC69IG	37	-714.6431	1519.8273	0.0000	1.0000
GTR	43	-710.5927	1530.2586	0.0000	1.0000
K2P	36	-722.7707	1533.1204	0.0000	1.0000
SYM	40	-720.6806	1541.0019	0.0000	1.0000
F81	38	-748.5796	1590.6976	0.0000	1.0000
JC69	35	-757.6403	1599.9317	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-664.5629	1411.1258	0.4473	0.4473
HKYI	40	-665.7553	1411.5106	0.3690	0.8163
HKYG	40	-667.2409	1414.4818	0.0835	0.8998
GTRIG	45	-662.8206	1415.6412	0.0468	0.9466
GTRI	44	-664.0077	1416.0153	0.0388	0.9854
GTRG	44	-665.7472	1419.4944	0.0068	0.9922
K2PIG	38	-672.8678	1421.7356	0.0022	0.9944
SYMIG	42	-668.9211	1421.8421	0.0021	0.9965
SYMI	41	-670.0673	1422.1345	0.0018	0.9983
K2PI	37	-674.5113	1423.0227	0.0012	0.9995
SYMG	41	-671.7972	1425.5945	0.0003	0.9998
K2PG	37	-676.4603	1426.9207	0.0002	1.0000
F81G	39	-707.3907	1492.7813	0.0000	1.0000
F81I	39	-707.4382	1492.8765	0.0000	1.0000
F81IG	40	-707.2425	1494.4849	0.0000	1.0000
HKY	39	-710.9360	1499.8719	0.0000	1.0000
JC69G	36	-714.8139	1501.6278	0.0000	1.0000
JC69I	36	-714.8297	1501.6594	0.0000	1.0000
JC69IG	37	-714.6431	1503.2861	0.0000	1.0000
GTR	43	-710.5927	1507.1854	0.0000	1.0000
K2P	36	-722.7707	1517.5415	0.0000	1.0000
SYM	40	-720.6806	1521.3612	0.0000	1.0000
F81	38	-748.5796	1573.1592	0.0000	1.0000
JC69	35	-757.6403	1585.2805	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-665.7553	1545.0121	0.4618	0.4618
K2PI	37	-674.5113	1546.5116	0.2182	0.6799
HKYIG	41	-664.5629	1547.9648	0.1055	0.7854
HKYG	40	-667.2409	1547.9833	0.1045	0.8900
K2PIG	38	-672.8678	1548.5620	0.0783	0.9682
K2PG	37	-676.4603	1550.4096	0.0311	0.9993
SYMI	41	-670.0673	1558.9736	0.0004	0.9997
SYMIG	42	-668.9211	1562.0187	0.0001	0.9998
SYMG	41	-671.7972	1562.4335	0.0001	0.9999
GTRI	44	-664.0077	1562.8670	0.0001	1.0000
GTRIG	45	-662.8206	1565.8304	0.0000	1.0000
GTRG	44	-665.7472	1566.3460	0.0000	1.0000
JC69G	36	-714.8139	1621.7792	0.0000	1.0000
JC69I	36	-714.8297	1621.8108	0.0000	1.0000
F81G	39	-707.3907	1622.9453	0.0000	1.0000
F81I	39	-707.4382	1623.0404	0.0000	1.0000
JC69IG	37	-714.6431	1626.7750	0.0000	1.0000
F81IG	40	-707.2425	1627.9864	0.0000	1.0000
HKY	39	-710.9360	1630.0359	0.0000	1.0000
K2P	36	-722.7707	1637.6928	0.0000	1.0000
GTR	43	-710.5927	1650.6995	0.0000	1.0000
SYM	40	-720.6806	1654.8627	0.0000	1.0000
F81	38	-748.5796	1699.9856	0.0000	1.0000
JC69	35	-757.6403	1702.0943	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/chr2_25794.phylip = 1 - 208;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25794.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25794.phylip = 1 - 208;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25794.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25794.phylip = 1 - 208;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25794.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;


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End of Output

