
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:08 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_32294.phylip" (19 taxa, 204 characters)

Minimum AIC  model: GTRG
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	-597.8485	1295.8198	0.4194	0.4194
HKYI	40	-598.1478	1296.4183	0.3109	0.7303
HKYIG	41	-597.8564	1298.9721	0.0867	0.8170
HKY	39	-601.0725	1299.1695	0.0786	0.8955
GTRG	44	-593.7112	1300.3281	0.0440	0.9395
GTRI	44	-594.0951	1301.0958	0.0300	0.9695
GTR	43	-596.8818	1303.4136	0.0094	0.9789
GTRIG	45	-593.8131	1303.8288	0.0076	0.9866
K2PG	37	-606.6362	1304.2121	0.0063	0.9929
K2PI	37	-606.8864	1304.7127	0.0049	0.9978
K2PIG	38	-606.6410	1307.2457	0.0014	0.9992
K2P	36	-610.2914	1308.5350	0.0007	0.9999
SYMG	41	-605.6311	1314.5215	0.0000	1.0000
SYMI	41	-605.9911	1315.2414	0.0000	1.0000
SYMIG	42	-605.6351	1317.7050	0.0000	1.0000
SYM	40	-609.0264	1318.1755	0.0000	1.0000
F81G	39	-611.3078	1319.6400	0.0000	1.0000
F81I	39	-611.6690	1320.3624	0.0000	1.0000
F81IG	40	-611.3187	1322.7602	0.0000	1.0000
F81	38	-614.7153	1323.3943	0.0000	1.0000
JC69G	36	-619.4846	1326.9212	0.0000	1.0000
JC69I	36	-619.7864	1327.5249	0.0000	1.0000
JC69IG	37	-619.4913	1329.9224	0.0000	1.0000
JC69	35	-623.1627	1331.3254	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-593.7112	1275.4225	0.2460	0.2460
HKYG	40	-597.8485	1275.6971	0.2145	0.4605
GTRI	44	-594.0951	1276.1901	0.1676	0.6281
HKYI	40	-598.1478	1276.2956	0.1590	0.7872
GTRIG	45	-593.8131	1277.6263	0.0817	0.8689
HKYIG	41	-597.8564	1277.7128	0.0783	0.9472
GTR	43	-596.8818	1279.7636	0.0281	0.9753
HKY	39	-601.0725	1280.1451	0.0232	0.9985
K2PG	37	-606.6362	1287.2723	0.0007	0.9991
K2PI	37	-606.8864	1287.7729	0.0005	0.9996
K2PIG	38	-606.6410	1289.2820	0.0002	0.9999
K2P	36	-610.2914	1292.5829	0.0000	0.9999
SYMG	41	-605.6311	1293.2622	0.0000	1.0000
SYMI	41	-605.9911	1293.9822	0.0000	1.0000
SYMIG	42	-605.6351	1295.2702	0.0000	1.0000
SYM	40	-609.0264	1298.0528	0.0000	1.0000
F81G	39	-611.3078	1300.6156	0.0000	1.0000
F81I	39	-611.6690	1301.3380	0.0000	1.0000
F81IG	40	-611.3187	1302.6375	0.0000	1.0000
F81	38	-614.7153	1305.4306	0.0000	1.0000
JC69G	36	-619.4846	1310.9691	0.0000	1.0000
JC69I	36	-619.7864	1311.5728	0.0000	1.0000
JC69IG	37	-619.4913	1312.9826	0.0000	1.0000
JC69	35	-623.1627	1316.3254	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-597.8485	1408.4219	0.2968	0.2968
HKYI	40	-598.1478	1409.0204	0.2201	0.5169
HKY	39	-601.0725	1409.5518	0.1687	0.6856
K2PG	37	-606.6362	1410.0428	0.1320	0.8176
K2PI	37	-606.8864	1410.5433	0.1028	0.9204
K2P	36	-610.2914	1412.0352	0.0487	0.9691
HKYIG	41	-597.8564	1413.7557	0.0206	0.9897
K2PIG	38	-606.6410	1415.3706	0.0092	0.9989
GTRG	44	-593.7112	1421.4198	0.0004	0.9994
GTRI	44	-594.0951	1422.1874	0.0003	0.9997
GTR	43	-596.8818	1422.4427	0.0003	0.9999
GTRIG	45	-593.8131	1426.9417	0.0000	1.0000
SYMG	41	-605.6311	1429.3052	0.0000	1.0000
F81G	39	-611.3078	1430.0223	0.0000	1.0000
SYMI	41	-605.9911	1430.0251	0.0000	1.0000
JC69G	36	-619.4846	1430.4214	0.0000	1.0000
F81I	39	-611.6690	1430.7447	0.0000	1.0000
SYM	40	-609.0264	1430.7776	0.0000	1.0000
JC69I	36	-619.7864	1431.0252	0.0000	1.0000
F81	38	-614.7153	1431.5192	0.0000	1.0000
JC69	35	-623.1627	1432.4596	0.0000	1.0000
SYMIG	42	-605.6351	1434.6313	0.0000	1.0000
F81IG	40	-611.3187	1435.3623	0.0000	1.0000
JC69IG	37	-619.4913	1435.7530	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/chr1_32294.phylip = 1 - 204;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32294.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32294.phylip = 1 - 204;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32294.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/chr1_32294.phylip = 1 - 204;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32294.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

