
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:44 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/chr7_11511.phylip" (19 taxa, 600 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-1522.3917	3130.6510	0.1920	0.1920
HKYG	40	-1522.4966	3130.8608	0.1728	0.3648
GTRG	44	-1517.9072	3130.9495	0.1653	0.5301
GTRIG	45	-1516.7620	3130.9970	0.1615	0.6916
HKYIG	41	-1521.4496	3131.0712	0.1556	0.8472
GTRI	44	-1517.9860	3131.1072	0.1528	1.0000
K2PG	37	-1545.8253	3170.6541	0.0000	1.0000
K2PI	37	-1545.9165	3170.8366	0.0000	1.0000
K2PIG	38	-1545.0734	3171.4303	0.0000	1.0000
SYMG	41	-1543.4950	3175.1620	0.0000	1.0000
SYMI	41	-1543.6377	3175.4474	0.0000	1.0000
SYMIG	42	-1542.6995	3175.8838	0.0000	1.0000
HKY	39	-1550.7858	3185.1431	0.0000	1.0000
GTR	43	-1546.5158	3185.8374	0.0000	1.0000
F81G	39	-1557.1087	3197.7889	0.0000	1.0000
F81I	39	-1557.2574	3198.0861	0.0000	1.0000
F81IG	40	-1556.3333	3198.5342	0.0000	1.0000
K2P	36	-1574.0715	3224.8747	0.0000	1.0000
SYM	40	-1571.2249	3228.3175	0.0000	1.0000
JC69G	36	-1576.6779	3230.0875	0.0000	1.0000
JC69I	36	-1576.8278	3230.3873	0.0000	1.0000
JC69IG	37	-1575.9349	3230.8734	0.0000	1.0000
F81	38	-1583.6080	3248.4995	0.0000	1.0000
JC69	35	-1603.8672	3282.2024	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1516.7620	3123.5241	0.2393	0.2393
GTRG	44	-1517.9072	3123.8143	0.2069	0.4462
GTRI	44	-1517.9860	3123.9721	0.1912	0.6374
HKYI	40	-1522.3917	3124.7834	0.1275	0.7649
HKYIG	41	-1521.4496	3124.8991	0.1203	0.8852
HKYG	40	-1522.4966	3124.9931	0.1148	1.0000
K2PG	37	-1545.8253	3165.6506	0.0000	1.0000
K2PI	37	-1545.9165	3165.8330	0.0000	1.0000
K2PIG	38	-1545.0734	3166.1469	0.0000	1.0000
SYMG	41	-1543.4950	3168.9900	0.0000	1.0000
SYMI	41	-1543.6377	3169.2753	0.0000	1.0000
SYMIG	42	-1542.6995	3169.3990	0.0000	1.0000
GTR	43	-1546.5158	3179.0317	0.0000	1.0000
HKY	39	-1550.7858	3179.5717	0.0000	1.0000
F81G	39	-1557.1087	3192.2175	0.0000	1.0000
F81I	39	-1557.2574	3192.5147	0.0000	1.0000
F81IG	40	-1556.3333	3192.6665	0.0000	1.0000
K2P	36	-1574.0715	3220.1429	0.0000	1.0000
SYM	40	-1571.2249	3222.4498	0.0000	1.0000
JC69G	36	-1576.6779	3225.3557	0.0000	1.0000
JC69I	36	-1576.8278	3225.6555	0.0000	1.0000
JC69IG	37	-1575.9349	3225.8698	0.0000	1.0000
F81	38	-1583.6080	3243.2161	0.0000	1.0000
JC69	35	-1603.8672	3277.7344	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1522.3917	3300.6606	0.4986	0.4986
HKYG	40	-1522.4966	3300.8703	0.4489	0.9475
HKYIG	41	-1521.4496	3305.1732	0.0522	0.9997
GTRG	44	-1517.9072	3317.2792	0.0001	0.9999
GTRI	44	-1517.9860	3317.4370	0.0001	1.0000
GTRIG	45	-1516.7620	3321.3859	0.0000	1.0000
K2PG	37	-1545.8253	3328.3370	0.0000	1.0000
K2PI	37	-1545.9165	3328.5194	0.0000	1.0000
K2PIG	38	-1545.0734	3333.2302	0.0000	1.0000
SYMG	41	-1543.4950	3349.2641	0.0000	1.0000
SYMI	41	-1543.6377	3349.5495	0.0000	1.0000
HKY	39	-1550.7858	3351.0519	0.0000	1.0000
SYMIG	42	-1542.6995	3354.0701	0.0000	1.0000
F81G	39	-1557.1087	3363.6977	0.0000	1.0000
F81I	39	-1557.2574	3363.9950	0.0000	1.0000
GTR	43	-1546.5158	3368.0997	0.0000	1.0000
F81IG	40	-1556.3333	3368.5437	0.0000	1.0000
K2P	36	-1574.0715	3378.4324	0.0000	1.0000
JC69G	36	-1576.6779	3383.6452	0.0000	1.0000
JC69I	36	-1576.8278	3383.9450	0.0000	1.0000
JC69IG	37	-1575.9349	3388.5562	0.0000	1.0000
SYM	40	-1571.2249	3398.3270	0.0000	1.0000
F81	38	-1583.6080	3410.2994	0.0000	1.0000
JC69	35	-1603.8672	3431.6269	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11511.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11511.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11511.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11511.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11511.phylip = 1 - 600;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11511.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

