
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:15 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/chrZ_4750.phylip" (19 taxa, 355 characters)

Minimum AIC  model: GTR
Minimum AICc model: HKY
Minimum BIC  model: HKY


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
HKY	39	-727.7840	1543.4729	0.3717	0.3717
HKYI	40	-727.3218	1545.0895	0.1656	0.5373
HKYG	40	-727.4087	1545.2632	0.1518	0.6891
GTR	43	-723.6144	1545.3960	0.1421	0.8312
GTRI	44	-723.2429	1547.2601	0.0559	0.8871
GTRG	44	-723.3360	1547.4461	0.0510	0.9381
HKYIG	41	-727.3247	1547.6525	0.0460	0.9841
GTRIG	45	-723.2455	1549.8890	0.0150	0.9991
F81	38	-735.7315	1556.8428	0.0005	0.9996
F81I	39	-735.4118	1558.7285	0.0002	0.9998
F81G	39	-735.4561	1558.8169	0.0002	0.9999
F81IG	40	-735.4117	1561.2693	0.0001	1.0000
K2P	36	-755.7897	1591.9568	0.0000	1.0000
K2PI	37	-755.3881	1593.6469	0.0000	1.0000
K2PG	37	-755.4332	1593.7371	0.0000	1.0000
SYM	40	-752.6434	1595.7326	0.0000	1.0000
K2PIG	38	-755.3902	1596.1602	0.0000	1.0000
SYMI	41	-752.3798	1597.7628	0.0000	1.0000
SYMG	41	-752.4096	1597.8224	0.0000	1.0000
SYMIG	42	-752.3828	1600.3425	0.0000	1.0000
JC69	35	-761.9666	1601.8329	0.0000	1.0000
JC69I	36	-761.6291	1603.6357	0.0000	1.0000
JC69G	36	-761.6601	1603.6976	0.0000	1.0000
JC69IG	37	-761.6535	1606.1776	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTR	43	-723.6144	1533.2288	0.2389	0.2389
HKY	39	-727.7840	1533.5681	0.2016	0.4405
GTRI	44	-723.2429	1534.4859	0.1274	0.5679
HKYI	40	-727.3218	1534.6437	0.1177	0.6856
GTRG	44	-723.3360	1534.6719	0.1161	0.8017
HKYG	40	-727.4087	1534.8174	0.1079	0.9096
GTRIG	45	-723.2455	1536.4909	0.0468	0.9564
HKYIG	41	-727.3247	1536.6493	0.0432	0.9996
F81	38	-735.7315	1547.4630	0.0002	0.9998
F81I	39	-735.4118	1548.8237	0.0001	0.9999
F81G	39	-735.4561	1548.9122	0.0001	1.0000
F81IG	40	-735.4117	1550.8235	0.0000	1.0000
K2P	36	-755.7897	1583.5795	0.0000	1.0000
K2PI	37	-755.3881	1584.7762	0.0000	1.0000
K2PG	37	-755.4332	1584.8664	0.0000	1.0000
SYM	40	-752.6434	1585.2868	0.0000	1.0000
SYMI	41	-752.3798	1586.7596	0.0000	1.0000
K2PIG	38	-755.3902	1586.7805	0.0000	1.0000
SYMG	41	-752.4096	1586.8192	0.0000	1.0000
SYMIG	42	-752.3828	1588.7656	0.0000	1.0000
JC69	35	-761.9666	1593.9333	0.0000	1.0000
JC69I	36	-761.6291	1595.2583	0.0000	1.0000
JC69G	36	-761.6601	1595.3203	0.0000	1.0000
JC69IG	37	-761.6535	1597.3070	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-727.7840	1684.5807	0.8516	0.8516
HKYI	40	-727.3218	1689.5284	0.0718	0.9234
HKYG	40	-727.4087	1689.7021	0.0658	0.9892
F81	38	-735.7315	1694.6035	0.0057	0.9949
HKYIG	41	-727.3247	1695.4062	0.0038	0.9987
GTR	43	-723.6144	1699.7299	0.0004	0.9991
F81I	39	-735.4118	1699.8363	0.0004	0.9995
F81G	39	-735.4561	1699.9248	0.0004	0.9999
GTRI	44	-723.2429	1704.8591	0.0000	0.9999
GTRG	44	-723.3360	1705.0451	0.0000	1.0000
F81IG	40	-735.4117	1705.7082	0.0000	1.0000
GTRIG	45	-723.2455	1710.7362	0.0000	1.0000
K2P	36	-755.7897	1722.9757	0.0000	1.0000
K2PI	37	-755.3881	1728.0446	0.0000	1.0000
K2PG	37	-755.4332	1728.1348	0.0000	1.0000
JC69	35	-761.9666	1729.4574	0.0000	1.0000
K2PIG	38	-755.3902	1733.9209	0.0000	1.0000
JC69I	36	-761.6291	1734.6545	0.0000	1.0000
JC69G	36	-761.6601	1734.7165	0.0000	1.0000
SYM	40	-752.6434	1740.1715	0.0000	1.0000
JC69IG	37	-761.6535	1740.5753	0.0000	1.0000
SYMI	41	-752.3798	1745.5164	0.0000	1.0000
SYMG	41	-752.4096	1745.5761	0.0000	1.0000
SYMIG	42	-752.3828	1751.3945	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4750.phylip = 1 - 355;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4750.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=equal;
 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);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4750.phylip = 1 - 355;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4750.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4750.phylip = 1 - 355;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4750.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

