
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:56 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_9143.phylip" (19 taxa, 506 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	-1567.8886	3222.8310	0.4294	0.4294
HKYI	40	-1567.9426	3222.9389	0.4068	0.8362
HKYIG	41	-1567.7535	3224.9294	0.1504	0.9865
GTRG	44	-1567.3210	3231.2320	0.0064	0.9930
GTRI	44	-1567.5425	3231.6751	0.0052	0.9981
GTRIG	45	-1567.3521	3233.7041	0.0019	1.0000
HKY	39	-1591.0256	3266.7465	0.0000	1.0000
K2PG	37	-1595.3312	3270.6709	0.0000	1.0000
K2PIG	38	-1595.2419	3272.8307	0.0000	1.0000
K2PI	37	-1596.8212	3273.6510	0.0000	1.0000
GTR	43	-1590.9657	3276.1218	0.0000	1.0000
SYMI	41	-1593.9552	3277.3329	0.0000	1.0000
F81G	39	-1596.6902	3278.0757	0.0000	1.0000
F81I	39	-1596.7826	3278.2605	0.0000	1.0000
F81IG	40	-1596.5709	3280.1955	0.0000	1.0000
SYMG	41	-1595.5242	3280.4708	0.0000	1.0000
SYMIG	42	-1595.3744	3282.5501	0.0000	1.0000
JC69G	36	-1618.4975	3314.6751	0.0000	1.0000
F81	38	-1617.5228	3317.3924	0.0000	1.0000
K2P	36	-1619.9030	3317.4862	0.0000	1.0000
SYM	40	-1616.0378	3319.1295	0.0000	1.0000
JC69I	36	-1621.3248	3320.3298	0.0000	1.0000
JC69IG	37	-1620.7237	3321.4560	0.0000	1.0000
JC69	35	-1639.4342	3354.2300	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1567.8886	3215.7772	0.4101	0.4101
HKYI	40	-1567.9426	3215.8851	0.3886	0.7987
HKYIG	41	-1567.7535	3217.5069	0.1727	0.9714
GTRG	44	-1567.3210	3222.6420	0.0133	0.9847
GTRI	44	-1567.5425	3223.0850	0.0106	0.9953
GTRIG	45	-1567.3521	3224.7041	0.0047	1.0000
HKY	39	-1591.0256	3260.0512	0.0000	1.0000
K2PG	37	-1595.3312	3264.6623	0.0000	1.0000
K2PIG	38	-1595.2419	3266.4838	0.0000	1.0000
K2PI	37	-1596.8212	3267.6424	0.0000	1.0000
GTR	43	-1590.9657	3267.9313	0.0000	1.0000
SYMI	41	-1593.9552	3269.9104	0.0000	1.0000
F81G	39	-1596.6902	3271.3805	0.0000	1.0000
F81I	39	-1596.7826	3271.5653	0.0000	1.0000
SYMG	41	-1595.5242	3273.0484	0.0000	1.0000
F81IG	40	-1596.5709	3273.1418	0.0000	1.0000
SYMIG	42	-1595.3744	3274.7488	0.0000	1.0000
JC69G	36	-1618.4975	3308.9949	0.0000	1.0000
F81	38	-1617.5228	3311.0455	0.0000	1.0000
K2P	36	-1619.9030	3311.8060	0.0000	1.0000
SYM	40	-1616.0378	3312.0757	0.0000	1.0000
JC69I	36	-1621.3248	3314.6496	0.0000	1.0000
JC69IG	37	-1620.7237	3315.4474	0.0000	1.0000
JC69	35	-1639.4342	3348.8683	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1567.8886	3384.8387	0.5004	0.5004
HKYI	40	-1567.9426	3384.9466	0.4741	0.9745
HKYIG	41	-1567.7535	3390.7949	0.0255	1.0000
GTRG	44	-1567.3210	3408.6096	0.0000	1.0000
GTRI	44	-1567.5425	3409.0527	0.0000	1.0000
GTRIG	45	-1567.3521	3414.8983	0.0000	1.0000
K2PG	37	-1595.3312	3421.0442	0.0000	1.0000
K2PI	37	-1596.8212	3424.0243	0.0000	1.0000
HKY	39	-1591.0256	3424.8861	0.0000	1.0000
K2PIG	38	-1595.2419	3427.0922	0.0000	1.0000
F81G	39	-1596.6902	3436.2154	0.0000	1.0000
F81I	39	-1596.7826	3436.4002	0.0000	1.0000
F81IG	40	-1596.5709	3442.2032	0.0000	1.0000
SYMI	41	-1593.9552	3443.1984	0.0000	1.0000
SYMG	41	-1595.5242	3446.3364	0.0000	1.0000
GTR	43	-1590.9657	3449.6724	0.0000	1.0000
SYMIG	42	-1595.3744	3452.2633	0.0000	1.0000
JC69G	36	-1618.4975	3461.1502	0.0000	1.0000
K2P	36	-1619.9030	3463.9613	0.0000	1.0000
JC69I	36	-1621.3248	3466.8049	0.0000	1.0000
F81	38	-1617.5228	3471.6539	0.0000	1.0000
JC69IG	37	-1620.7237	3471.8293	0.0000	1.0000
SYM	40	-1616.0378	3481.1372	0.0000	1.0000
JC69	35	-1639.4342	3496.7971	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/chr7_9143.phylip = 1 - 506;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9143.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/chr7_9143.phylip = 1 - 506;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9143.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/chr7_9143.phylip = 1 - 506;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_9143.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

