
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:28 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_11901.phylip" (19 taxa, 558 characters)

Minimum AIC  model: HKYG
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	-1519.6833	3125.7109	0.4284	0.4284
HKYI	40	-1520.0276	3126.3994	0.3036	0.7320
HKYIG	41	-1519.0888	3126.8520	0.2421	0.9741
GTRG	44	-1518.4895	3132.6984	0.0130	0.9871
GTRI	44	-1519.0270	3133.7733	0.0076	0.9947
GTRIG	45	-1518.2024	3134.4908	0.0053	1.0000
HKY	39	-1536.6856	3157.3943	0.0000	1.0000
K2PG	37	-1540.7400	3160.8876	0.0000	1.0000
K2PI	37	-1541.3915	3162.1906	0.0000	1.0000
K2PIG	38	-1540.3481	3162.4071	0.0000	1.0000
GTR	43	-1535.5963	3164.5544	0.0000	1.0000
SYMG	41	-1539.8266	3168.3276	0.0000	1.0000
SYMI	41	-1540.3892	3169.4528	0.0000	1.0000
SYMIG	42	-1539.4454	3169.9044	0.0000	1.0000
F81G	39	-1548.6644	3181.3519	0.0000	1.0000
F81I	39	-1548.9986	3182.0204	0.0000	1.0000
F81IG	40	-1548.0624	3182.4690	0.0000	1.0000
K2P	36	-1558.3916	3193.8965	0.0000	1.0000
SYM	40	-1557.7458	3201.8359	0.0000	1.0000
F81	38	-1564.7477	3211.2064	0.0000	1.0000
JC69G	36	-1567.3910	3211.8953	0.0000	1.0000
JC69I	36	-1568.0622	3213.2377	0.0000	1.0000
JC69IG	37	-1567.0452	3213.4982	0.0000	1.0000
JC69	35	-1583.8647	3242.5570	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1519.6833	3119.3666	0.3999	0.3999
HKYI	40	-1520.0276	3120.0551	0.2834	0.6833
HKYIG	41	-1519.0888	3120.1775	0.2666	0.9499
GTRG	44	-1518.4895	3124.9791	0.0242	0.9740
GTRI	44	-1519.0270	3126.0540	0.0141	0.9882
GTRIG	45	-1518.2024	3126.4049	0.0118	1.0000
HKY	39	-1536.6856	3151.3711	0.0000	1.0000
K2PG	37	-1540.7400	3155.4799	0.0000	1.0000
K2PIG	38	-1540.3481	3156.6961	0.0000	1.0000
K2PI	37	-1541.3915	3156.7829	0.0000	1.0000
GTR	43	-1535.5963	3157.1925	0.0000	1.0000
SYMG	41	-1539.8266	3161.6531	0.0000	1.0000
SYMI	41	-1540.3892	3162.7784	0.0000	1.0000
SYMIG	42	-1539.4454	3162.8908	0.0000	1.0000
F81G	39	-1548.6644	3175.3287	0.0000	1.0000
F81I	39	-1548.9986	3175.9972	0.0000	1.0000
F81IG	40	-1548.0624	3176.1247	0.0000	1.0000
K2P	36	-1558.3916	3188.7833	0.0000	1.0000
SYM	40	-1557.7458	3195.4916	0.0000	1.0000
F81	38	-1564.7477	3205.4954	0.0000	1.0000
JC69G	36	-1567.3910	3206.7821	0.0000	1.0000
JC69IG	37	-1567.0452	3208.0905	0.0000	1.0000
JC69I	36	-1568.0622	3208.1244	0.0000	1.0000
JC69	35	-1583.8647	3237.7294	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1519.6833	3292.3409	0.5601	0.5601
HKYI	40	-1520.0276	3293.0295	0.3969	0.9570
HKYIG	41	-1519.0888	3297.4763	0.0430	1.0000
GTRG	44	-1518.4895	3315.2509	0.0000	1.0000
K2PG	37	-1540.7400	3315.4812	0.0000	1.0000
GTRI	44	-1519.0270	3316.3258	0.0000	1.0000
K2PI	37	-1541.3915	3316.7842	0.0000	1.0000
HKY	39	-1536.6856	3320.0211	0.0000	1.0000
GTRIG	45	-1518.2024	3321.0011	0.0000	1.0000
K2PIG	38	-1540.3481	3321.0218	0.0000	1.0000
SYMG	41	-1539.8266	3338.9519	0.0000	1.0000
SYMI	41	-1540.3892	3340.0771	0.0000	1.0000
GTR	43	-1535.5963	3343.1400	0.0000	1.0000
F81G	39	-1548.6644	3343.9787	0.0000	1.0000
K2P	36	-1558.3916	3344.4602	0.0000	1.0000
SYMIG	42	-1539.4454	3344.5139	0.0000	1.0000
F81I	39	-1548.9986	3344.6472	0.0000	1.0000
F81IG	40	-1548.0624	3349.0991	0.0000	1.0000
JC69G	36	-1567.3910	3362.4590	0.0000	1.0000
JC69I	36	-1568.0622	3363.8014	0.0000	1.0000
JC69IG	37	-1567.0452	3368.0917	0.0000	1.0000
SYM	40	-1557.7458	3368.4660	0.0000	1.0000
F81	38	-1564.7477	3369.8210	0.0000	1.0000
JC69	35	-1583.8647	3389.0820	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/chrZ_11901.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11901.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/chrZ_11901.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11901.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/chrZ_11901.phylip = 1 - 558;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11901.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

