
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:24 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/chr1_35494.phylip" (19 taxa, 125 characters)

Minimum AIC  model: HKYG
Minimum AICc model: F81G
Minimum BIC  model: F81G


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
F81G	39	-282.0721	678.8501	0.3124	0.3124
F81I	39	-282.1058	678.9175	0.3020	0.6144
HKYG	40	-280.8745	680.7966	0.1180	0.7324
HKYI	40	-280.8979	680.8434	0.1153	0.8477
F81	38	-285.5887	681.6424	0.0773	0.9251
F81IG	40	-282.0316	683.1108	0.0371	0.9622
HKY	39	-284.6995	684.1048	0.0226	0.9847
HKYIG	41	-280.8338	685.1616	0.0133	0.9980
JC69G	36	-294.7622	691.7971	0.0005	0.9985
JC69I	36	-294.7931	691.8590	0.0005	0.9990
GTRG	44	-277.2386	691.9772	0.0004	0.9994
K2PG	37	-294.1541	694.6301	0.0001	0.9996
K2PI	37	-294.1787	694.6792	0.0001	0.9997
JC69	35	-298.2218	694.7582	0.0001	0.9998
GTRI	44	-278.7306	694.9611	0.0001	0.9999
JC69IG	37	-294.7234	695.7687	0.0001	0.9999
K2P	36	-297.7455	697.7637	0.0000	1.0000
K2PIG	38	-294.1204	698.7059	0.0000	1.0000
GTR	43	-283.5470	699.8101	0.0000	1.0000
GTRIG	45	-278.7044	699.8139	0.0000	1.0000
SYMG	41	-292.0260	707.5460	0.0000	1.0000
SYMI	41	-292.0490	707.5920	0.0000	1.0000
SYM	40	-295.9552	710.9580	0.0000	1.0000
SYMIG	42	-291.9707	711.9901	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-280.8745	641.7490	0.1877	0.1877
HKYI	40	-280.8979	641.7958	0.1833	0.3710
F81G	39	-282.0721	642.1442	0.1540	0.5251
F81I	39	-282.1058	642.2117	0.1489	0.6740
GTRG	44	-277.2386	642.4772	0.1304	0.8044
HKYIG	41	-280.8338	643.6676	0.0719	0.8763
F81IG	40	-282.0316	644.0632	0.0590	0.9353
GTRI	44	-278.7306	645.4611	0.0293	0.9647
F81	38	-285.5887	647.1773	0.0124	0.9771
HKY	39	-284.6995	647.3989	0.0111	0.9882
GTRIG	45	-278.7044	647.4088	0.0111	0.9993
GTR	43	-283.5470	653.0941	0.0006	1.0000
JC69G	36	-294.7622	661.5244	0.0000	1.0000
JC69I	36	-294.7931	661.5863	0.0000	1.0000
K2PG	37	-294.1541	662.3082	0.0000	1.0000
K2PI	37	-294.1787	662.3574	0.0000	1.0000
JC69IG	37	-294.7234	663.4468	0.0000	1.0000
K2PIG	38	-294.1204	664.2408	0.0000	1.0000
SYMG	41	-292.0260	666.0520	0.0000	1.0000
SYMI	41	-292.0490	666.0980	0.0000	1.0000
JC69	35	-298.2218	666.4436	0.0000	1.0000
K2P	36	-297.7455	667.4910	0.0000	1.0000
SYMIG	42	-291.9707	667.9413	0.0000	1.0000
SYM	40	-295.9552	671.9104	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
F81G	39	-282.0721	752.4485	0.3236	0.3236
F81I	39	-282.1058	752.5159	0.3128	0.6364
F81	38	-285.5887	754.6532	0.1074	0.7439
HKYG	40	-280.8745	754.8816	0.0959	0.8397
HKYI	40	-280.8979	754.9283	0.0936	0.9333
F81IG	40	-282.0316	757.1957	0.0301	0.9635
HKY	39	-284.6995	757.7031	0.0234	0.9869
HKYIG	41	-280.8338	759.6285	0.0089	0.9958
JC69G	36	-294.7622	763.3437	0.0014	0.9972
JC69I	36	-294.7931	763.4056	0.0014	0.9985
JC69	35	-298.2218	765.4345	0.0005	0.9990
GTRG	44	-277.2386	766.9230	0.0002	0.9993
K2PG	37	-294.1541	766.9558	0.0002	0.9995
K2PI	37	-294.1787	767.0050	0.0002	0.9997
JC69IG	37	-294.7234	768.0944	0.0001	0.9998
K2P	36	-297.7455	769.3103	0.0001	0.9999
GTRI	44	-278.7306	769.9069	0.0001	1.0000
K2PIG	38	-294.1204	771.7167	0.0000	1.0000
GTRIG	45	-278.7044	774.6829	0.0000	1.0000
GTR	43	-283.5470	774.7116	0.0000	1.0000
SYMG	41	-292.0260	782.0129	0.0000	1.0000
SYMI	41	-292.0490	782.0589	0.0000	1.0000
SYM	40	-295.9552	785.0430	0.0000	1.0000
SYMIG	42	-291.9707	786.7305	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/chr1_35494.phylip = 1 - 125;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_35494.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 (F81G)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_35494.phylip = 1 - 125;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_35494.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=1 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (F81G)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_35494.phylip = 1 - 125;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_35494.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=1 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


-------------------------------------------------------------
End of Output

