
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:05 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/chr2_8146.phylip" (19 taxa, 203 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	-577.4897	1255.2263	0.5383	0.5383
HKYI	40	-577.9734	1256.1938	0.3318	0.8701
HKYIG	41	-577.4570	1258.3053	0.1155	0.9855
GTRG	44	-575.5111	1264.0855	0.0064	0.9919
HKY	39	-584.0928	1265.3267	0.0034	0.9954
GTRI	44	-576.2197	1265.5026	0.0032	0.9986
GTRIG	45	-575.4840	1267.3374	0.0013	0.9998
GTR	43	-581.1365	1272.0718	0.0001	0.9999
K2PG	37	-591.7243	1274.4911	0.0000	1.0000
K2PI	37	-592.4474	1275.9372	0.0000	1.0000
K2PIG	38	-591.6616	1277.3964	0.0000	1.0000
K2P	36	-597.5472	1283.1425	0.0000	1.0000
SYMG	41	-590.0520	1283.4953	0.0000	1.0000
SYMI	41	-590.9357	1285.2627	0.0000	1.0000
SYMIG	42	-590.0117	1286.5983	0.0000	1.0000
SYM	40	-595.1455	1290.5379	0.0000	1.0000
F81G	39	-599.4176	1295.9764	0.0000	1.0000
F81I	39	-600.0544	1297.2498	0.0000	1.0000
F81IG	40	-599.3808	1299.0085	0.0000	1.0000
F81	38	-605.0811	1304.2355	0.0000	1.0000
JC69G	36	-610.2864	1308.6211	0.0000	1.0000
JC69I	36	-610.9724	1309.9930	0.0000	1.0000
JC69IG	37	-610.2358	1311.5140	0.0000	1.0000
JC69	35	-616.0135	1317.1168	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-577.4897	1234.9794	0.4446	0.4446
HKYI	40	-577.9734	1235.9469	0.2741	0.7186
HKYIG	41	-577.4570	1236.9140	0.1690	0.8876
GTRG	44	-575.5111	1239.0222	0.0589	0.9465
GTRI	44	-576.2197	1240.4393	0.0290	0.9755
GTRIG	45	-575.4840	1240.9679	0.0223	0.9978
HKY	39	-584.0928	1246.1856	0.0016	0.9994
GTR	43	-581.1365	1248.2730	0.0006	1.0000
K2PG	37	-591.7243	1257.4487	0.0000	1.0000
K2PI	37	-592.4474	1258.8948	0.0000	1.0000
K2PIG	38	-591.6616	1259.3232	0.0000	1.0000
SYMG	41	-590.0520	1262.1040	0.0000	1.0000
SYMI	41	-590.9357	1263.8714	0.0000	1.0000
SYMIG	42	-590.0117	1264.0233	0.0000	1.0000
K2P	36	-597.5472	1267.0943	0.0000	1.0000
SYM	40	-595.1455	1270.2910	0.0000	1.0000
F81G	39	-599.4176	1276.8353	0.0000	1.0000
F81I	39	-600.0544	1278.1087	0.0000	1.0000
F81IG	40	-599.3808	1278.7616	0.0000	1.0000
F81	38	-605.0811	1286.1623	0.0000	1.0000
JC69G	36	-610.2864	1292.5729	0.0000	1.0000
JC69I	36	-610.9724	1293.9448	0.0000	1.0000
JC69IG	37	-610.2358	1294.4716	0.0000	1.0000
JC69	35	-616.0135	1302.0270	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-577.4897	1367.5076	0.5842	0.5842
HKYI	40	-577.9734	1368.4751	0.3602	0.9444
HKYIG	41	-577.4570	1372.7554	0.0424	0.9868
HKY	39	-584.0928	1375.4007	0.0113	0.9981
K2PG	37	-591.7243	1380.0373	0.0011	0.9992
K2PI	37	-592.4474	1381.4834	0.0005	0.9997
GTRG	44	-575.5111	1384.8033	0.0001	0.9998
K2PIG	38	-591.6616	1385.2250	0.0001	0.9999
GTRI	44	-576.2197	1386.2204	0.0001	0.9999
K2P	36	-597.5472	1386.3697	0.0000	1.0000
GTRIG	45	-575.4840	1390.0622	0.0000	1.0000
GTR	43	-581.1365	1390.7409	0.0000	1.0000
SYMG	41	-590.0520	1397.9455	0.0000	1.0000
SYMI	41	-590.9357	1399.7128	0.0000	1.0000
SYM	40	-595.1455	1402.8192	0.0000	1.0000
SYMIG	42	-590.0117	1403.1780	0.0000	1.0000
F81G	39	-599.4176	1406.0503	0.0000	1.0000
F81I	39	-600.0544	1407.3238	0.0000	1.0000
F81IG	40	-599.3808	1411.2898	0.0000	1.0000
JC69G	36	-610.2864	1411.8483	0.0000	1.0000
F81	38	-605.0811	1412.0641	0.0000	1.0000
JC69I	36	-610.9724	1413.2202	0.0000	1.0000
JC69IG	37	-610.2358	1417.0602	0.0000	1.0000
JC69	35	-616.0135	1417.9892	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/chr2_8146.phylip = 1 - 203;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8146.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/chr2_8146.phylip = 1 - 203;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8146.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/chr2_8146.phylip = 1 - 203;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8146.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;


-------------------------------------------------------------
End of Output

