
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:30 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/chr1_5483.phylip" (19 taxa, 768 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
Minimum BIC  model: K2PG


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
SYMG	41	-3202.0222	6490.7882	0.5974	0.5974
SYMIG	42	-3201.9694	6492.9208	0.2057	0.8031
GTRIG	45	-3199.0386	6493.8113	0.1318	0.9348
GTRG	44	-3200.9669	6495.4110	0.0592	0.9941
K2PG	37	-3212.1567	6502.1655	0.0020	0.9961
HKYG	40	-3209.2316	6502.9750	0.0013	0.9974
GTRI	44	-3205.3347	6504.1467	0.0008	0.9982
K2PIG	38	-3212.0666	6504.1991	0.0007	0.9989
SYMI	41	-3208.9656	6504.6749	0.0006	0.9995
HKYIG	41	-3209.0801	6504.9041	0.0005	1.0000
K2PI	37	-3219.3875	6516.6272	0.0000	1.0000
HKYI	40	-3216.0819	6516.6756	0.0000	1.0000
GTR	43	-3240.3188	6571.8641	0.0000	1.0000
SYM	40	-3244.0801	6572.6718	0.0000	1.0000
K2P	36	-3257.4388	6590.5220	0.0000	1.0000
HKY	39	-3255.0284	6592.3426	0.0000	1.0000
F81IG	40	-3272.1187	6628.7492	0.0000	1.0000
JC69IG	37	-3275.5247	6628.9014	0.0000	1.0000
JC69G	36	-3277.3680	6630.3803	0.0000	1.0000
F81G	39	-3274.4496	6631.1849	0.0000	1.0000
JC69I	36	-3281.6696	6638.9835	0.0000	1.0000
F81I	39	-3278.4646	6639.2149	0.0000	1.0000
JC69	35	-3316.8634	6707.1693	0.0000	1.0000
F81	38	-3314.3353	6708.7365	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-3202.0222	6486.0444	0.5259	0.5259
SYMIG	42	-3201.9694	6487.9388	0.2040	0.7299
GTRIG	45	-3199.0386	6488.0772	0.1903	0.9202
GTRG	44	-3200.9669	6489.9338	0.0752	0.9954
K2PG	37	-3212.1567	6498.3134	0.0011	0.9966
HKYG	40	-3209.2316	6498.4633	0.0011	0.9976
GTRI	44	-3205.3347	6498.6695	0.0010	0.9986
SYMI	41	-3208.9656	6499.9311	0.0005	0.9991
K2PIG	38	-3212.0666	6500.1332	0.0005	0.9995
HKYIG	41	-3209.0801	6500.1603	0.0005	1.0000
HKYI	40	-3216.0819	6512.1639	0.0000	1.0000
K2PI	37	-3219.3875	6512.7751	0.0000	1.0000
GTR	43	-3240.3188	6566.6376	0.0000	1.0000
SYM	40	-3244.0801	6568.1601	0.0000	1.0000
K2P	36	-3257.4388	6586.8777	0.0000	1.0000
HKY	39	-3255.0284	6588.0569	0.0000	1.0000
F81IG	40	-3272.1187	6624.2375	0.0000	1.0000
JC69IG	37	-3275.5247	6625.0493	0.0000	1.0000
JC69G	36	-3277.3680	6626.7359	0.0000	1.0000
F81G	39	-3274.4496	6626.8992	0.0000	1.0000
F81I	39	-3278.4646	6634.9292	0.0000	1.0000
JC69I	36	-3281.6696	6635.3392	0.0000	1.0000
JC69	35	-3316.8634	6703.7267	0.0000	1.0000
F81	38	-3314.3353	6704.6707	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-3212.1567	6670.1337	0.9212	0.9212
SYMG	41	-3202.0222	6676.4398	0.0394	0.9606
K2PIG	38	-3212.0666	6676.5972	0.0364	0.9969
SYMIG	42	-3201.9694	6682.9779	0.0015	0.9984
HKYG	40	-3209.2316	6684.2148	0.0008	0.9993
K2PI	37	-3219.3875	6684.5953	0.0007	0.9999
SYMI	41	-3208.9656	6690.3265	0.0000	1.0000
HKYIG	41	-3209.0801	6690.5557	0.0000	1.0000
GTRG	44	-3200.9669	6694.2605	0.0000	1.0000
GTRIG	45	-3199.0386	6697.0477	0.0000	1.0000
HKYI	40	-3216.0819	6697.9155	0.0000	1.0000
GTRI	44	-3205.3347	6702.9962	0.0000	1.0000
SYM	40	-3244.0801	6753.9117	0.0000	1.0000
K2P	36	-3257.4388	6754.0541	0.0000	1.0000
GTR	43	-3240.3188	6766.3206	0.0000	1.0000
HKY	39	-3255.0284	6769.1647	0.0000	1.0000
JC69G	36	-3277.3680	6793.9124	0.0000	1.0000
JC69IG	37	-3275.5247	6796.8696	0.0000	1.0000
JC69I	36	-3281.6696	6802.5156	0.0000	1.0000
F81G	39	-3274.4496	6808.0070	0.0000	1.0000
F81IG	40	-3272.1187	6809.9890	0.0000	1.0000
F81I	39	-3278.4646	6816.0370	0.0000	1.0000
JC69	35	-3316.8634	6866.2593	0.0000	1.0000
F81	38	-3314.3353	6881.1347	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5483.phylip = 1 - 768;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5483.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5483.phylip = 1 - 768;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5483.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=Fixed(Equal);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5483.phylip = 1 - 768;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5483.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

