
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:24 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_7889.phylip" (19 taxa, 570 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1386.5121	2868.5670	0.3182	0.3182
GTRI	44	-1386.7485	2869.0398	0.2512	0.5694
SYMG	41	-1390.8862	2870.2951	0.1341	0.7035
GTRIG	45	-1386.2156	2870.3319	0.1317	0.8352
SYMI	41	-1391.1228	2870.7683	0.1059	0.9410
SYMIG	42	-1390.5464	2871.9467	0.0587	0.9998
K2PG	37	-1403.0563	2885.3982	0.0001	0.9998
HKYG	40	-1400.1419	2886.4842	0.0000	0.9999
K2PIG	38	-1402.4570	2886.4960	0.0000	0.9999
HKYI	40	-1400.2761	2886.7526	0.0000	1.0000
HKYIG	41	-1399.4647	2887.4521	0.0000	1.0000
K2PI	37	-1404.4302	2888.1461	0.0000	1.0000
GTR	43	-1405.7724	2904.7387	0.0000	1.0000
SYM	40	-1409.9327	2906.0657	0.0000	1.0000
K2P	36	-1424.5428	2926.0838	0.0000	1.0000
HKY	39	-1421.2013	2926.2894	0.0000	1.0000
JC69G	36	-1438.1552	2953.3085	0.0000	1.0000
JC69I	36	-1438.3336	2953.6654	0.0000	1.0000
JC69IG	37	-1437.4445	2954.1747	0.0000	1.0000
F81G	39	-1435.8065	2955.4998	0.0000	1.0000
F81I	39	-1435.9899	2955.8667	0.0000	1.0000
F81IG	40	-1435.0884	2956.3772	0.0000	1.0000
JC69	35	-1458.5455	2991.8102	0.0000	1.0000
F81	38	-1456.1791	2993.9401	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1386.5121	2861.0242	0.3487	0.3487
GTRI	44	-1386.7485	2861.4970	0.2752	0.6239
GTRIG	45	-1386.2156	2862.4311	0.1725	0.7964
SYMG	41	-1390.8862	2863.7724	0.0882	0.8847
SYMI	41	-1391.1228	2864.2456	0.0696	0.9543
SYMIG	42	-1390.5464	2865.0928	0.0456	0.9999
K2PG	37	-1403.0563	2880.1125	0.0000	0.9999
HKYG	40	-1400.1419	2880.2838	0.0000	0.9999
HKYI	40	-1400.2761	2880.5522	0.0000	1.0000
K2PIG	38	-1402.4570	2880.9141	0.0000	1.0000
HKYIG	41	-1399.4647	2880.9293	0.0000	1.0000
K2PI	37	-1404.4302	2882.8604	0.0000	1.0000
GTR	43	-1405.7724	2897.5448	0.0000	1.0000
SYM	40	-1409.9327	2899.8654	0.0000	1.0000
HKY	39	-1421.2013	2920.4026	0.0000	1.0000
K2P	36	-1424.5428	2921.0857	0.0000	1.0000
JC69G	36	-1438.1552	2948.3104	0.0000	1.0000
JC69I	36	-1438.3336	2948.6673	0.0000	1.0000
JC69IG	37	-1437.4445	2948.8890	0.0000	1.0000
F81G	39	-1435.8065	2949.6130	0.0000	1.0000
F81I	39	-1435.9899	2949.9799	0.0000	1.0000
F81IG	40	-1435.0884	2950.1768	0.0000	1.0000
JC69	35	-1458.5455	2987.0911	0.0000	1.0000
F81	38	-1456.1791	2988.3581	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1403.0563	3040.9011	0.4105	0.4105
SYMG	41	-1390.8862	3041.9435	0.2438	0.6543
SYMI	41	-1391.1228	3042.4167	0.1924	0.8467
K2PI	37	-1404.4302	3043.6489	0.1039	0.9506
K2PIG	38	-1402.4570	3046.0483	0.0313	0.9819
SYMIG	42	-1390.5464	3047.6095	0.0143	0.9963
GTRG	44	-1386.5121	3052.2322	0.0014	0.9977
GTRI	44	-1386.7485	3052.7050	0.0011	0.9988
HKYG	40	-1400.1419	3054.1093	0.0006	0.9994
HKYI	40	-1400.2761	3054.3777	0.0005	0.9999
GTRIG	45	-1386.2156	3057.9848	0.0001	1.0000
HKYIG	41	-1399.4647	3059.1004	0.0000	1.0000
SYM	40	-1409.9327	3073.6908	0.0000	1.0000
K2P	36	-1424.5428	3077.5286	0.0000	1.0000
GTR	43	-1405.7724	3084.4071	0.0000	1.0000
HKY	39	-1421.2013	3089.8824	0.0000	1.0000
JC69G	36	-1438.1552	3104.7533	0.0000	1.0000
JC69I	36	-1438.3336	3105.1102	0.0000	1.0000
JC69IG	37	-1437.4445	3109.6776	0.0000	1.0000
F81G	39	-1435.8065	3119.0928	0.0000	1.0000
F81I	39	-1435.9899	3119.4597	0.0000	1.0000
F81IG	40	-1435.0884	3124.0022	0.0000	1.0000
JC69	35	-1458.5455	3139.1883	0.0000	1.0000
F81	38	-1456.1791	3153.4923	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/chrZ_7889.phylip = 1 - 570;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7889.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/chrZ_7889.phylip = 1 - 570;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7889.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7889.phylip = 1 - 570;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_7889.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

