
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:17 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/chr4_13110.phylip" (19 taxa, 378 characters)

Minimum AIC  model: GTRG
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	-1600.5444	3290.8217	0.3585	0.3585
HKYIG	41	-1599.6581	3291.5662	0.2471	0.6055
HKYI	40	-1601.5559	3292.8448	0.1304	0.7359
GTRG	44	-1596.4905	3292.8729	0.1285	0.8644
GTRIG	45	-1595.7188	3293.9074	0.0766	0.9411
GTRI	44	-1597.2703	3294.4325	0.0589	1.0000
GTR	43	-1623.8321	3344.9935	0.0000	1.0000
HKY	39	-1631.1174	3349.4657	0.0000	1.0000
F81G	39	-1635.3618	3357.9543	0.0000	1.0000
F81IG	40	-1634.8893	3359.5115	0.0000	1.0000
F81I	39	-1636.4455	3360.1217	0.0000	1.0000
SYMG	41	-1643.0131	3378.2763	0.0000	1.0000
K2PG	37	-1648.0412	3378.3530	0.0000	1.0000
K2PIG	38	-1647.7828	3380.3089	0.0000	1.0000
SYMIG	42	-1642.9125	3380.6071	0.0000	1.0000
K2PI	37	-1650.4003	3383.0712	0.0000	1.0000
SYMI	41	-1645.9187	3384.0874	0.0000	1.0000
F81	38	-1660.0603	3404.8640	0.0000	1.0000
JC69G	36	-1673.3391	3426.4905	0.0000	1.0000
JC69IG	37	-1673.0095	3428.2897	0.0000	1.0000
JC69I	36	-1675.0150	3429.8423	0.0000	1.0000
SYM	40	-1670.3993	3430.5315	0.0000	1.0000
K2P	36	-1676.9872	3433.7868	0.0000	1.0000
JC69	35	-1699.0948	3475.5580	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1596.4905	3280.9810	0.2277	0.2277
HKYG	40	-1600.5444	3281.0888	0.2157	0.4434
HKYIG	41	-1599.6581	3281.3162	0.1925	0.6360
GTRIG	45	-1595.7188	3281.4375	0.1812	0.8172
GTRI	44	-1597.2703	3282.5406	0.1044	0.9215
HKYI	40	-1601.5559	3283.1118	0.0785	1.0000
GTR	43	-1623.8321	3333.6642	0.0000	1.0000
HKY	39	-1631.1174	3340.2349	0.0000	1.0000
F81G	39	-1635.3618	3348.7235	0.0000	1.0000
F81IG	40	-1634.8893	3349.7786	0.0000	1.0000
F81I	39	-1636.4455	3350.8909	0.0000	1.0000
SYMG	41	-1643.0131	3368.0263	0.0000	1.0000
SYMIG	42	-1642.9125	3369.8250	0.0000	1.0000
K2PG	37	-1648.0412	3370.0825	0.0000	1.0000
K2PIG	38	-1647.7828	3371.5655	0.0000	1.0000
SYMI	41	-1645.9187	3373.8374	0.0000	1.0000
K2PI	37	-1650.4003	3374.8006	0.0000	1.0000
F81	38	-1660.0603	3396.1207	0.0000	1.0000
JC69G	36	-1673.3391	3418.6782	0.0000	1.0000
JC69IG	37	-1673.0095	3420.0191	0.0000	1.0000
SYM	40	-1670.3993	3420.7985	0.0000	1.0000
JC69I	36	-1675.0150	3422.0300	0.0000	1.0000
K2P	36	-1676.9872	3425.9745	0.0000	1.0000
JC69	35	-1699.0948	3468.1896	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1600.5444	3438.4845	0.6716	0.6716
HKYI	40	-1601.5559	3440.5076	0.2442	0.9158
HKYIG	41	-1599.6581	3442.6469	0.0838	0.9996
GTRG	44	-1596.4905	3454.1163	0.0003	0.9998
GTRI	44	-1597.2703	3455.6760	0.0001	1.0000
GTRIG	45	-1595.7188	3458.5078	0.0000	1.0000
HKY	39	-1631.1174	3493.6958	0.0000	1.0000
F81G	39	-1635.3618	3502.1844	0.0000	1.0000
GTR	43	-1623.8321	3502.8646	0.0000	1.0000
F81I	39	-1636.4455	3504.3518	0.0000	1.0000
F81IG	40	-1634.8893	3507.1743	0.0000	1.0000
K2PG	37	-1648.0412	3515.6735	0.0000	1.0000
K2PI	37	-1650.4003	3520.3917	0.0000	1.0000
K2PIG	38	-1647.7828	3521.0915	0.0000	1.0000
SYMG	41	-1643.0131	3529.3569	0.0000	1.0000
SYMIG	42	-1642.9125	3535.0905	0.0000	1.0000
SYMI	41	-1645.9187	3535.1680	0.0000	1.0000
F81	38	-1660.0603	3545.6467	0.0000	1.0000
JC69G	36	-1673.3391	3560.3344	0.0000	1.0000
JC69I	36	-1675.0150	3563.6862	0.0000	1.0000
JC69IG	37	-1673.0095	3565.6102	0.0000	1.0000
K2P	36	-1676.9872	3567.6307	0.0000	1.0000
SYM	40	-1670.3993	3578.1943	0.0000	1.0000
JC69	35	-1699.0948	3605.9109	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/chr4_13110.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13110.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13110.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13110.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/chr4_13110.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13110.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

