
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:12 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_6727.phylip" (19 taxa, 642 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-1509.5735	3106.8871	0.6854	0.6854
HKYI	40	-1511.6801	3108.8178	0.2610	0.9464
GTRIG	45	-1507.9441	3112.8345	0.0350	0.9814
GTRI	44	-1510.0955	3114.8241	0.0130	0.9944
K2PIG	38	-1518.3307	3117.5767	0.0033	0.9977
K2PI	37	-1520.2467	3119.1491	0.0015	0.9992
HKYG	40	-1517.8246	3121.1067	0.0006	0.9997
SYMIG	42	-1516.7477	3123.5255	0.0002	0.9999
SYMI	41	-1518.4765	3124.6930	0.0001	1.0000
GTRG	44	-1516.5733	3127.7798	0.0000	1.0000
K2PG	37	-1526.5647	3131.7850	0.0000	1.0000
SYMG	41	-1525.2855	3138.3110	0.0000	1.0000
F81IG	40	-1528.3867	3142.2310	0.0000	1.0000
F81I	39	-1529.8573	3142.8973	0.0000	1.0000
JC69IG	37	-1536.4240	3151.5036	0.0000	1.0000
JC69I	36	-1537.7630	3151.9293	0.0000	1.0000
F81G	39	-1535.5243	3154.2314	0.0000	1.0000
JC69G	36	-1543.5446	3163.4926	0.0000	1.0000
HKY	39	-1563.0784	3209.3395	0.0000	1.0000
GTR	43	-1562.3561	3217.0399	0.0000	1.0000
K2P	36	-1571.8746	3220.1525	0.0000	1.0000
SYM	40	-1571.1956	3227.8488	0.0000	1.0000
F81	38	-1580.0190	3240.9534	0.0000	1.0000
JC69	35	-1588.1669	3250.4923	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1509.5735	3101.1471	0.6853	0.6853
HKYI	40	-1511.6801	3103.3602	0.2266	0.9119
GTRIG	45	-1507.9441	3105.8882	0.0640	0.9759
GTRI	44	-1510.0955	3108.1910	0.0202	0.9962
K2PIG	38	-1518.3307	3112.6613	0.0022	0.9983
K2PI	37	-1520.2467	3114.4935	0.0009	0.9992
HKYG	40	-1517.8246	3115.6491	0.0005	0.9997
SYMIG	42	-1516.7477	3117.4954	0.0002	0.9999
SYMI	41	-1518.4765	3118.9530	0.0001	1.0000
GTRG	44	-1516.5733	3121.1466	0.0000	1.0000
K2PG	37	-1526.5647	3127.1294	0.0000	1.0000
SYMG	41	-1525.2855	3132.5710	0.0000	1.0000
F81IG	40	-1528.3867	3136.7735	0.0000	1.0000
F81I	39	-1529.8573	3137.7146	0.0000	1.0000
JC69IG	37	-1536.4240	3146.8480	0.0000	1.0000
JC69I	36	-1537.7630	3147.5260	0.0000	1.0000
F81G	39	-1535.5243	3149.0487	0.0000	1.0000
JC69G	36	-1543.5446	3159.0893	0.0000	1.0000
HKY	39	-1563.0784	3204.1568	0.0000	1.0000
GTR	43	-1562.3561	3210.7121	0.0000	1.0000
K2P	36	-1571.8746	3215.7492	0.0000	1.0000
SYM	40	-1571.1956	3222.3912	0.0000	1.0000
F81	38	-1580.0190	3236.0379	0.0000	1.0000
JC69	35	-1588.1669	3246.3339	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-1520.2467	3279.6832	0.5888	0.5888
HKYI	40	-1511.6801	3281.9437	0.1902	0.7789
K2PIG	38	-1518.3307	3282.3157	0.1579	0.9368
HKYIG	41	-1509.5735	3284.1952	0.0617	0.9985
K2PG	37	-1526.5647	3292.3191	0.0011	0.9996
HKYG	40	-1517.8246	3294.2327	0.0004	1.0000
SYMI	41	-1518.4765	3302.0011	0.0000	1.0000
GTRI	44	-1510.0955	3304.6329	0.0000	1.0000
SYMIG	42	-1516.7477	3305.0081	0.0000	1.0000
GTRIG	45	-1507.9441	3306.7947	0.0000	1.0000
JC69I	36	-1537.7630	3308.2512	0.0000	1.0000
F81I	39	-1529.8573	3311.8335	0.0000	1.0000
JC69IG	37	-1536.4240	3312.0377	0.0000	1.0000
F81IG	40	-1528.3867	3315.3570	0.0000	1.0000
SYMG	41	-1525.2855	3315.6191	0.0000	1.0000
GTRG	44	-1516.5733	3317.5885	0.0000	1.0000
JC69G	36	-1543.5446	3319.8145	0.0000	1.0000
F81G	39	-1535.5243	3323.1676	0.0000	1.0000
K2P	36	-1571.8746	3376.4744	0.0000	1.0000
HKY	39	-1563.0784	3378.2757	0.0000	1.0000
SYM	40	-1571.1956	3400.9748	0.0000	1.0000
JC69	35	-1588.1669	3402.5945	0.0000	1.0000
GTR	43	-1562.3561	3402.6894	0.0000	1.0000
F81	38	-1580.0190	3405.6923	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/chrZ_6727.phylip = 1 - 642;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6727.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 (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6727.phylip = 1 - 642;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6727.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 BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6727.phylip = 1 - 642;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_6727.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;


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End of Output

