
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:24 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_11558.phylip" (19 taxa, 359 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1551.7011	3193.7167	0.9132	0.9132
HKYIG	41	-1553.3320	3199.5284	0.0500	0.9632
GTRG	44	-1549.8669	3200.3452	0.0332	0.9964
GTRIG	45	-1551.4072	3206.0413	0.0019	0.9983
HKYI	40	-1558.0162	3206.3469	0.0017	0.9999
GTRI	44	-1556.2644	3213.1402	0.0001	1.0000
K2PG	37	-1573.0783	3228.9166	0.0000	1.0000
HKY	39	-1572.0944	3231.9694	0.0000	1.0000
K2PIG	38	-1574.6593	3234.5812	0.0000	1.0000
SYMG	41	-1572.9098	3238.6839	0.0000	1.0000
K2PI	37	-1579.3678	3241.4958	0.0000	1.0000
GTR	43	-1572.8319	3243.6765	0.0000	1.0000
SYMIG	42	-1574.5251	3244.4805	0.0000	1.0000
SYMI	41	-1579.0718	3251.0080	0.0000	1.0000
K2P	36	-1596.1490	3272.5713	0.0000	1.0000
SYM	40	-1596.0971	3282.5087	0.0000	1.0000
F81G	39	-1613.9493	3315.6792	0.0000	1.0000
F81IG	40	-1616.6066	3323.5277	0.0000	1.0000
F81I	39	-1618.6211	3325.0229	0.0000	1.0000
JC69G	36	-1632.9016	3346.0765	0.0000	1.0000
JC69IG	37	-1632.9028	3348.5658	0.0000	1.0000
JC69I	36	-1636.4486	3353.1704	0.0000	1.0000
F81	38	-1635.8634	3356.9893	0.0000	1.0000
JC69	35	-1652.2319	3382.2657	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1551.7011	3183.4022	0.8349	0.8349
GTRG	44	-1549.8669	3187.7337	0.0957	0.9307
HKYIG	41	-1553.3320	3188.6641	0.0601	0.9908
GTRIG	45	-1551.4072	3192.8145	0.0075	0.9983
HKYI	40	-1558.0162	3196.0325	0.0015	0.9998
GTRI	44	-1556.2644	3200.5288	0.0002	1.0000
K2PG	37	-1573.0783	3220.1565	0.0000	1.0000
HKY	39	-1572.0944	3222.1889	0.0000	1.0000
K2PIG	38	-1574.6593	3225.3187	0.0000	1.0000
SYMG	41	-1572.9098	3227.8196	0.0000	1.0000
GTR	43	-1572.8319	3231.6638	0.0000	1.0000
K2PI	37	-1579.3678	3232.7357	0.0000	1.0000
SYMIG	42	-1574.5251	3233.0502	0.0000	1.0000
SYMI	41	-1579.0718	3240.1437	0.0000	1.0000
K2P	36	-1596.1490	3264.2980	0.0000	1.0000
SYM	40	-1596.0971	3272.1943	0.0000	1.0000
F81G	39	-1613.9493	3305.8987	0.0000	1.0000
F81IG	40	-1616.6066	3313.2132	0.0000	1.0000
F81I	39	-1618.6211	3315.2423	0.0000	1.0000
JC69G	36	-1632.9016	3337.8032	0.0000	1.0000
JC69IG	37	-1632.9028	3339.8057	0.0000	1.0000
JC69I	36	-1636.4486	3344.8971	0.0000	1.0000
F81	38	-1635.8634	3347.7268	0.0000	1.0000
JC69	35	-1652.2319	3374.4638	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1551.7011	3338.7351	0.9880	0.9880
HKYIG	41	-1553.3320	3347.8803	0.0102	0.9982
HKYI	40	-1558.0162	3351.3654	0.0018	0.9999
GTRG	44	-1549.8669	3358.5999	0.0000	1.0000
K2PG	37	-1573.0783	3363.8394	0.0000	1.0000
GTRIG	45	-1551.4072	3367.5640	0.0000	1.0000
GTRI	44	-1556.2644	3371.3950	0.0000	1.0000
K2PIG	38	-1574.6593	3372.8850	0.0000	1.0000
HKY	39	-1572.0944	3373.6384	0.0000	1.0000
K2PI	37	-1579.3678	3376.4186	0.0000	1.0000
SYMG	41	-1572.9098	3387.0358	0.0000	1.0000
SYMIG	42	-1574.5251	3396.1497	0.0000	1.0000
GTR	43	-1572.8319	3398.6467	0.0000	1.0000
SYMI	41	-1579.0718	3399.3599	0.0000	1.0000
K2P	36	-1596.1490	3404.0976	0.0000	1.0000
SYM	40	-1596.0971	3427.5272	0.0000	1.0000
F81G	39	-1613.9493	3457.3482	0.0000	1.0000
F81I	39	-1618.6211	3466.6919	0.0000	1.0000
F81IG	40	-1616.6066	3468.5461	0.0000	1.0000
JC69G	36	-1632.9016	3477.6028	0.0000	1.0000
JC69IG	37	-1632.9028	3483.4886	0.0000	1.0000
JC69I	36	-1636.4486	3484.6967	0.0000	1.0000
F81	38	-1635.8634	3495.2931	0.0000	1.0000
JC69	35	-1652.2319	3510.3801	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/chrZ_11558.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11558.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/chrZ_11558.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11558.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11558.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11558.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

