
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:14 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_226.phylip" (19 taxa, 530 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1710.4517	3517.0684	0.5451	0.5451
GTRI	44	-1711.3726	3518.9102	0.2171	0.7622
GTRIG	45	-1710.4524	3519.4584	0.1650	0.9272
HKYG	40	-1717.7706	3522.2488	0.0409	0.9681
HKYI	40	-1718.5208	3523.7492	0.0193	0.9874
HKYIG	41	-1717.7708	3524.5991	0.0126	1.0000
K2PG	37	-1736.4058	3552.5271	0.0000	1.0000
K2PI	37	-1737.3676	3554.4506	0.0000	1.0000
K2PIG	38	-1736.3959	3554.8285	0.0000	1.0000
SYMG	41	-1733.2646	3555.5867	0.0000	1.0000
SYMI	41	-1734.3433	3557.7440	0.0000	1.0000
SYMIG	42	-1733.2592	3557.9352	0.0000	1.0000
GTR	43	-1738.1736	3570.1333	0.0000	1.0000
HKY	39	-1743.9590	3572.2854	0.0000	1.0000
K2P	36	-1763.0171	3603.4378	0.0000	1.0000
F81G	39	-1759.6053	3603.5780	0.0000	1.0000
F81I	39	-1760.3796	3605.1266	0.0000	1.0000
F81IG	40	-1759.6179	3605.9433	0.0000	1.0000
SYM	40	-1760.2272	3607.1621	0.0000	1.0000
JC69G	36	-1774.1376	3625.6789	0.0000	1.0000
JC69IG	37	-1773.6865	3627.0885	0.0000	1.0000
JC69I	36	-1774.9463	3627.2963	0.0000	1.0000
F81	38	-1785.1511	3652.3389	0.0000	1.0000
JC69	35	-1800.0437	3675.1885	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1710.4517	3508.9035	0.5457	0.5457
GTRI	44	-1711.3726	3510.7452	0.2173	0.7630
GTRIG	45	-1710.4524	3510.9047	0.2006	0.9637
HKYG	40	-1717.7706	3515.5412	0.0198	0.9834
HKYI	40	-1718.5208	3517.0416	0.0093	0.9927
HKYIG	41	-1717.7708	3517.5417	0.0073	1.0000
K2PG	37	-1736.4058	3546.8117	0.0000	1.0000
SYMG	41	-1733.2646	3548.5293	0.0000	1.0000
K2PI	37	-1737.3676	3548.7352	0.0000	1.0000
K2PIG	38	-1736.3959	3548.7918	0.0000	1.0000
SYMIG	42	-1733.2592	3550.5184	0.0000	1.0000
SYMI	41	-1734.3433	3550.6867	0.0000	1.0000
GTR	43	-1738.1736	3562.3473	0.0000	1.0000
HKY	39	-1743.9590	3565.9180	0.0000	1.0000
F81G	39	-1759.6053	3597.2106	0.0000	1.0000
K2P	36	-1763.0171	3598.0341	0.0000	1.0000
F81I	39	-1760.3796	3598.7593	0.0000	1.0000
F81IG	40	-1759.6179	3599.2358	0.0000	1.0000
SYM	40	-1760.2272	3600.4545	0.0000	1.0000
JC69G	36	-1774.1376	3620.2752	0.0000	1.0000
JC69IG	37	-1773.6865	3621.3730	0.0000	1.0000
JC69I	36	-1774.9463	3621.8926	0.0000	1.0000
F81	38	-1785.1511	3646.3023	0.0000	1.0000
JC69	35	-1800.0437	3670.0873	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1717.7706	3686.4563	0.6564	0.6564
HKYI	40	-1718.5208	3687.9567	0.3100	0.9663
HKYIG	41	-1717.7708	3692.7296	0.0285	0.9948
GTRG	44	-1710.4517	3696.9101	0.0035	0.9984
GTRI	44	-1711.3726	3698.7518	0.0014	0.9998
GTRIG	45	-1710.4524	3703.1842	0.0002	0.9999
K2PG	37	-1736.4058	3704.9081	0.0001	1.0000
K2PI	37	-1737.3676	3706.8316	0.0000	1.0000
K2PIG	38	-1736.3959	3711.1612	0.0000	1.0000
SYMG	41	-1733.2646	3723.7172	0.0000	1.0000
SYMI	41	-1734.3433	3725.8746	0.0000	1.0000
SYMIG	42	-1733.2592	3729.9792	0.0000	1.0000
HKY	39	-1743.9590	3732.5602	0.0000	1.0000
GTR	43	-1738.1736	3746.0810	0.0000	1.0000
K2P	36	-1763.0171	3751.8577	0.0000	1.0000
F81G	39	-1759.6053	3763.8528	0.0000	1.0000
F81I	39	-1760.3796	3765.4015	0.0000	1.0000
F81IG	40	-1759.6179	3770.1509	0.0000	1.0000
SYM	40	-1760.2272	3771.3696	0.0000	1.0000
JC69G	36	-1774.1376	3774.0988	0.0000	1.0000
JC69I	36	-1774.9463	3775.7162	0.0000	1.0000
JC69IG	37	-1773.6865	3779.4695	0.0000	1.0000
F81	38	-1785.1511	3808.6716	0.0000	1.0000
JC69	35	-1800.0437	3819.6380	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_226.phylip = 1 - 530;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_226.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 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) shapepr=Uniform(0.1,50.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_226.phylip = 1 - 530;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_226.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 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) 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/chr3_226.phylip = 1 - 530;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_226.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;


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

