
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:25 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/chr12_5678.phylip" (19 taxa, 1023 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-3415.2240	6922.4970	0.6470	0.6470
GTRIG	45	-3415.1408	6924.5192	0.2354	0.8825
GTRI	44	-3416.9296	6925.9083	0.1175	1.0000
HKYG	40	-3434.2011	6951.7422	0.0000	1.0000
HKYIG	41	-3434.1301	6953.7708	0.0000	1.0000
HKYI	40	-3436.6692	6956.6786	0.0000	1.0000
SYMG	41	-3443.3660	6972.2427	0.0000	1.0000
SYMIG	42	-3443.2979	6974.2814	0.0000	1.0000
SYMI	41	-3445.2369	6975.9845	0.0000	1.0000
K2PG	37	-3451.3611	6979.5771	0.0000	1.0000
K2PIG	38	-3451.2916	6981.5955	0.0000	1.0000
K2PI	37	-3454.2449	6985.3447	0.0000	1.0000
GTR	43	-3471.0480	7031.9611	0.0000	1.0000
HKY	39	-3487.5846	7056.3432	0.0000	1.0000
F81G	39	-3493.2995	7067.7730	0.0000	1.0000
F81IG	40	-3493.2427	7069.8254	0.0000	1.0000
F81I	39	-3495.8711	7072.9161	0.0000	1.0000
SYM	40	-3496.4714	7076.2829	0.0000	1.0000
K2P	36	-3504.7525	7084.2068	0.0000	1.0000
JC69G	36	-3506.0966	7086.8951	0.0000	1.0000
JC69IG	37	-3506.0387	7088.9322	0.0000	1.0000
JC69I	36	-3508.7300	7092.1618	0.0000	1.0000
F81	38	-3541.6188	7162.2497	0.0000	1.0000
JC69	35	-3554.6477	7181.8485	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3415.2240	6918.4480	0.6323	0.6323
GTRIG	45	-3415.1408	6920.2817	0.2528	0.8851
GTRI	44	-3416.9296	6921.8592	0.1149	1.0000
HKYG	40	-3434.2011	6948.4021	0.0000	1.0000
HKYIG	41	-3434.1301	6950.2601	0.0000	1.0000
HKYI	40	-3436.6692	6953.3384	0.0000	1.0000
SYMG	41	-3443.3660	6968.7320	0.0000	1.0000
SYMIG	42	-3443.2979	6970.5957	0.0000	1.0000
SYMI	41	-3445.2369	6972.4738	0.0000	1.0000
K2PG	37	-3451.3611	6976.7223	0.0000	1.0000
K2PIG	38	-3451.2916	6978.5833	0.0000	1.0000
K2PI	37	-3454.2449	6982.4899	0.0000	1.0000
GTR	43	-3471.0480	7028.0960	0.0000	1.0000
HKY	39	-3487.5846	7053.1692	0.0000	1.0000
F81G	39	-3493.2995	7064.5990	0.0000	1.0000
F81IG	40	-3493.2427	7066.4853	0.0000	1.0000
F81I	39	-3495.8711	7069.7421	0.0000	1.0000
SYM	40	-3496.4714	7072.9427	0.0000	1.0000
K2P	36	-3504.7525	7081.5050	0.0000	1.0000
JC69G	36	-3506.0966	7084.1933	0.0000	1.0000
JC69IG	37	-3506.0387	7086.0774	0.0000	1.0000
JC69I	36	-3508.7300	7089.4600	0.0000	1.0000
F81	38	-3541.6188	7159.2375	0.0000	1.0000
JC69	35	-3554.6477	7179.2953	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-3415.2240	7135.3897	0.8181	0.8181
GTRI	44	-3416.9296	7138.8009	0.1486	0.9667
GTRIG	45	-3415.1408	7142.1540	0.0278	0.9945
HKYG	40	-3434.2011	7145.6219	0.0049	0.9994
HKYI	40	-3436.6692	7150.5582	0.0004	0.9998
HKYIG	41	-3434.1301	7152.4104	0.0002	1.0000
K2PG	37	-3451.3611	7159.1506	0.0000	1.0000
K2PI	37	-3454.2449	7164.9182	0.0000	1.0000
K2PIG	38	-3451.2916	7165.9421	0.0000	1.0000
SYMG	41	-3443.3660	7170.8823	0.0000	1.0000
SYMI	41	-3445.2369	7174.6240	0.0000	1.0000
SYMIG	42	-3443.2979	7177.6765	0.0000	1.0000
GTR	43	-3471.0480	7240.1073	0.0000	1.0000
HKY	39	-3487.5846	7245.4585	0.0000	1.0000
F81G	39	-3493.2995	7256.8883	0.0000	1.0000
K2P	36	-3504.7525	7259.0028	0.0000	1.0000
JC69G	36	-3506.0966	7261.6911	0.0000	1.0000
F81I	39	-3495.8711	7262.0314	0.0000	1.0000
F81IG	40	-3493.2427	7263.7051	0.0000	1.0000
JC69I	36	-3508.7300	7266.9578	0.0000	1.0000
JC69IG	37	-3506.0387	7268.5057	0.0000	1.0000
SYM	40	-3496.4714	7270.1625	0.0000	1.0000
F81	38	-3541.6188	7346.5963	0.0000	1.0000
JC69	35	-3554.6477	7351.8626	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/chr12_5678.phylip = 1 - 1023;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5678.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/chr12_5678.phylip = 1 - 1023;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5678.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5678.phylip = 1 - 1023;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5678.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;


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End of Output

