
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:16 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_32363.phylip" (19 taxa, 207 characters)

Minimum AIC  model: HKY
Minimum AICc model: HKY
Minimum BIC  model: K2P


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
HKY	39	-621.1680	1339.0186	0.3095	0.3095
K2P	36	-626.1679	1340.0064	0.1889	0.4984
HKYI	40	-620.5095	1340.7780	0.1284	0.6268
HKYG	40	-620.5893	1340.9377	0.1186	0.7453
K2PI	37	-625.3177	1341.2744	0.1002	0.8455
K2PG	37	-625.4062	1341.4515	0.0917	0.9372
HKYIG	41	-620.5122	1343.8970	0.0270	0.9642
K2PIG	38	-625.3203	1344.2834	0.0223	0.9864
GTR	43	-618.8101	1346.8349	0.0062	0.9927
GTRI	44	-618.2911	1349.0266	0.0021	0.9947
GTRG	44	-618.3445	1349.1334	0.0020	0.9967
SYM	40	-624.9363	1349.6316	0.0015	0.9982
SYMI	41	-624.2784	1351.4296	0.0006	0.9989
SYMG	41	-624.3513	1351.5754	0.0006	0.9994
GTRIG	45	-618.2920	1352.2983	0.0004	0.9998
SYMIG	42	-624.2807	1354.5857	0.0001	1.0000
JC69	35	-637.8271	1360.3911	0.0000	1.0000
F81	38	-633.6307	1360.9042	0.0000	1.0000
JC69I	36	-636.9597	1361.5900	0.0000	1.0000
JC69G	36	-637.1797	1362.0300	0.0000	1.0000
F81I	39	-632.8661	1362.4149	0.0000	1.0000
F81G	39	-633.0296	1362.7419	0.0000	1.0000
JC69IG	37	-636.9703	1364.5796	0.0000	1.0000
F81IG	40	-632.8766	1365.5122	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKY	39	-621.1680	1320.3359	0.2839	0.2839
HKYI	40	-620.5095	1321.0189	0.2018	0.4857
HKYG	40	-620.5893	1321.1787	0.1863	0.6720
HKYIG	41	-620.5122	1323.0243	0.0740	0.7461
GTR	43	-618.8101	1323.6201	0.0550	0.8010
K2P	36	-626.1679	1324.3358	0.0384	0.8395
GTRI	44	-618.2911	1324.5822	0.0340	0.8734
K2PI	37	-625.3177	1324.6353	0.0331	0.9065
GTRG	44	-618.3445	1324.6889	0.0322	0.9387
K2PG	37	-625.4062	1324.8124	0.0303	0.9690
GTRIG	45	-618.2920	1326.5841	0.0125	0.9815
K2PIG	38	-625.3203	1326.6406	0.0121	0.9936
SYM	40	-624.9363	1329.8725	0.0024	0.9961
SYMI	41	-624.2784	1330.5569	0.0017	0.9978
SYMG	41	-624.3513	1330.7027	0.0016	0.9994
SYMIG	42	-624.2807	1332.5613	0.0006	1.0000
F81	38	-633.6307	1343.2613	0.0000	1.0000
F81I	39	-632.8661	1343.7322	0.0000	1.0000
F81G	39	-633.0296	1344.0592	0.0000	1.0000
JC69	35	-637.8271	1345.6542	0.0000	1.0000
F81IG	40	-632.8766	1345.7532	0.0000	1.0000
JC69I	36	-636.9597	1345.9194	0.0000	1.0000
JC69G	36	-637.1797	1346.3594	0.0000	1.0000
JC69IG	37	-636.9703	1347.9405	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-626.1679	1444.3137	0.7214	0.7214
K2PI	37	-625.3177	1447.9459	0.1173	0.8387
K2PG	37	-625.4062	1448.1230	0.1074	0.9461
HKY	39	-621.1680	1450.3120	0.0359	0.9820
K2PIG	38	-625.3203	1453.2839	0.0081	0.9902
HKYI	40	-620.5095	1454.3277	0.0048	0.9950
HKYG	40	-620.5893	1454.4875	0.0045	0.9995
HKYIG	41	-620.5122	1459.6658	0.0003	0.9998
JC69	35	-637.8271	1462.2994	0.0001	0.9999
SYM	40	-624.9363	1463.1813	0.0001	0.9999
JC69I	36	-636.9597	1465.8973	0.0000	1.0000
JC69G	36	-637.1797	1466.3373	0.0000	1.0000
GTR	43	-618.8101	1466.9270	0.0000	1.0000
SYMI	41	-624.2784	1467.1983	0.0000	1.0000
SYMG	41	-624.3513	1467.3442	0.0000	1.0000
F81	38	-633.6307	1469.9046	0.0000	1.0000
GTRI	44	-618.2911	1471.2218	0.0000	1.0000
JC69IG	37	-636.9703	1471.2511	0.0000	1.0000
GTRG	44	-618.3445	1471.3286	0.0000	1.0000
SYMIG	42	-624.2807	1472.5355	0.0000	1.0000
F81I	39	-632.8661	1473.7083	0.0000	1.0000
F81G	39	-633.0296	1474.0353	0.0000	1.0000
GTRIG	45	-618.2920	1476.5564	0.0000	1.0000
F81IG	40	-632.8766	1479.0619	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32363.phylip = 1 - 207;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32363.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32363.phylip = 1 - 207;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32363.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


[Mrbayes block for the best BIC model (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32363.phylip = 1 - 207;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32363.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


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End of Output

