
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:20 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_6203.phylip" (19 taxa, 216 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-602.9855	1304.7139	0.8325	0.8325
K2PG	37	-609.6344	1309.0665	0.0945	0.9270
HKYI	40	-605.8295	1310.4018	0.0484	0.9754
HKYIG	41	-605.8511	1313.4952	0.0103	0.9857
K2PI	37	-612.0587	1313.9152	0.0084	0.9941
GTRG	44	-602.6420	1316.4420	0.0024	0.9965
K2PIG	38	-612.0444	1316.8346	0.0019	0.9984
SYMG	41	-609.0064	1319.8060	0.0004	0.9988
F81G	39	-612.2914	1320.3101	0.0003	0.9992
GTRIG	45	-603.0684	1320.4897	0.0003	0.9995
GTRI	44	-605.2182	1321.5943	0.0002	0.9997
JC69G	36	-617.8117	1322.5061	0.0001	0.9998
K2P	36	-618.0402	1322.9630	0.0001	0.9999
F81I	39	-614.4090	1324.5453	0.0000	0.9999
SYMI	41	-611.5111	1324.8153	0.0000	1.0000
F81IG	40	-614.0105	1326.7639	0.0000	1.0000
JC69I	36	-620.2579	1327.3985	0.0000	1.0000
SYMIG	42	-611.3861	1327.6509	0.0000	1.0000
JC69IG	37	-619.4879	1328.7736	0.0000	1.0000
GTR	43	-611.8940	1331.7881	0.0000	1.0000
HKY	39	-618.1484	1332.0240	0.0000	1.0000
F81	38	-620.4334	1333.6125	0.0000	1.0000
JC69	35	-625.8982	1335.7964	0.0000	1.0000
SYM	40	-623.4716	1345.6862	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-602.9855	1285.9710	0.8744	0.8744
HKYI	40	-605.8295	1291.6589	0.0509	0.9253
K2PG	37	-609.6344	1293.2687	0.0228	0.9480
GTRG	44	-602.6420	1293.2841	0.0226	0.9706
HKYIG	41	-605.8511	1293.7021	0.0183	0.9889
GTRIG	45	-603.0684	1296.1368	0.0054	0.9943
K2PI	37	-612.0587	1298.1175	0.0020	0.9964
GTRI	44	-605.2182	1298.4364	0.0017	0.9981
SYMG	41	-609.0064	1300.0129	0.0008	0.9989
K2PIG	38	-612.0444	1300.0888	0.0008	0.9996
F81G	39	-612.2914	1302.5828	0.0002	0.9998
SYMI	41	-611.5111	1305.0222	0.0001	0.9999
SYMIG	42	-611.3861	1306.7723	0.0000	0.9999
F81I	39	-614.4090	1306.8180	0.0000	0.9999
JC69G	36	-617.8117	1307.6234	0.0000	1.0000
F81IG	40	-614.0105	1308.0210	0.0000	1.0000
K2P	36	-618.0402	1308.0804	0.0000	1.0000
GTR	43	-611.8940	1309.7881	0.0000	1.0000
JC69I	36	-620.2579	1312.5158	0.0000	1.0000
JC69IG	37	-619.4879	1312.9759	0.0000	1.0000
HKY	39	-618.1484	1314.2968	0.0000	1.0000
F81	38	-620.4334	1316.8667	0.0000	1.0000
JC69	35	-625.8982	1321.7964	0.0000	1.0000
SYM	40	-623.4716	1326.9433	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-609.6344	1418.1540	0.7347	0.7347
HKYG	40	-602.9855	1420.9821	0.1786	0.9133
K2PI	37	-612.0587	1423.0028	0.0650	0.9783
HKYI	40	-605.8295	1426.6701	0.0104	0.9887
K2PIG	38	-612.0444	1428.3494	0.0045	0.9932
JC69G	36	-617.8117	1429.1334	0.0030	0.9963
K2P	36	-618.0402	1429.5904	0.0024	0.9987
HKYIG	41	-605.8511	1432.0885	0.0007	0.9994
JC69I	36	-620.2579	1434.0258	0.0003	0.9996
F81G	39	-612.2914	1434.2187	0.0002	0.9999
JC69IG	37	-619.4879	1437.8612	0.0000	0.9999
SYMG	41	-609.0064	1438.3993	0.0000	0.9999
F81I	39	-614.4090	1438.4539	0.0000	1.0000
JC69	35	-625.8982	1439.9311	0.0000	1.0000
GTRG	44	-602.6420	1441.7963	0.0000	1.0000
F81IG	40	-614.0105	1443.0321	0.0000	1.0000
SYMI	41	-611.5111	1443.4087	0.0000	1.0000
F81	38	-620.4334	1445.1273	0.0000	1.0000
HKY	39	-618.1484	1445.9326	0.0000	1.0000
GTRI	44	-605.2182	1446.9486	0.0000	1.0000
GTRIG	45	-603.0684	1448.0243	0.0000	1.0000
SYMIG	42	-611.3861	1448.5340	0.0000	1.0000
GTR	43	-611.8940	1454.9251	0.0000	1.0000
SYM	40	-623.4716	1461.9544	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6203.phylip = 1 - 216;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6203.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 AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6203.phylip = 1 - 216;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6203.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6203.phylip = 1 - 216;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_6203.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

