BAli-Phy: MCMC Post-hoc Analysis

Data and model

Partition	Sequences	Lengths	Alphabet	Substitution Model	Indel Model	Scale Model
1	25.fasta	111 - 131	RNA	S1 `= GTR +> ASRV.Gamma(n=4) +> Inv +> Covarion.Huelsenbeck02`	I1 `= RS07`	scale1 `~ Gamma(0.5, 2)`

Scalar variables

Diagnostic flags: concerning; caution.

Statistic	Mean ± SD			Median (95% BCI)		ACT	ESS	burnin	PSRF-80%CI	PSRF-RCF
#indels	55.31	±	4.307	55	(47, 63)	15.04	19849.0	262.0	1.0	1.0
#substs	727.5	±	9.173	728	(710, 745)	45.18	6609.0	297.0	0.9863	1.002
RS07:meanLength	2.001	±	0.2473	1.972	(1.559, 2.494)	9.614	31060.0	205.0	1.0	1.0
RS07:rate	0.01522	±	0.003198	0.01504	(0.009149, 0.02143)	11.57	25813.0	330.0	1.0	1.0
P1/#indels	55.31	±	4.307	55	(47, 63)	15.04	19849.0	262.0	1.0	1.0
P1/#substs	727.5	±	9.173	728	(710, 745)	45.18	6609.0	297.0	0.9863	1.002
P1/likelihood	-2703	±	13.14	-2703	(-2728, -2677)	20.67	14445.0	349.0	1.0	1.0
P1/prior_A	-406.7	±	24.5	-405	(-455.9, -361.3)	17.47	17089.0	474.0	0.9993	1.0
P1/\|A\|	163.7	±	6.24	163	(152, 175)	82.24	3631.0	686.0	1.027	1.001
P1/\|indels\|	106.7	±	9.59	106	(89, 125)	24.44	12219.0	354.0	0.9825	1.0
ASRV.Gamma:alpha	989.9	±	1.737e+05	2.084	(0.9251, 4.661)	1.054	283188.0	218.0	1.0	1.001
Covarion.Huelsenbeck02:pi1	0.6438	±	0.05432	0.6433	(0.5376, 0.7506)	5.251	56865.0	249.0	0.9998	0.9999
Covarion.Huelsenbeck02:r	0.5756	±	0.1484	0.559	(0.3072, 0.8691)	9.087	32860.0	233.0	1.0	1.0
Covarion.Huelsenbeck02:rate	0.2603	±	0.06874	0.2527	(0.1373, 0.3983)	8.612	34674.0	287.0	1.0	1.0
Covarion.Huelsenbeck02:s01	0.3709	±	0.1029	0.3579	(0.1914, 0.5776)	8.746	34144.0	212.0	0.9999	0.9999
Covarion.Huelsenbeck02:s10	0.2047	±	0.06063	0.1971	(0.09755, 0.3264)	7.802	38275.0	240.0	1.0	0.9999
GTR:pi[A]	0.2112	±	0.01944	0.2101	(0.1742, 0.25)	16.37	18237.0	629.0	1.0	1.0
GTR:pi[C]	0.2748	±	0.01974	0.2744	(0.2365, 0.3136)	11.14	26803.0	407.0	0.9999	1.0
GTR:pi[G]	0.2997	±	0.02509	0.2991	(0.2509, 0.3492)	16.93	17637.0	727.0	1.001	1.001
GTR:pi[U]	0.2144	±	0.01698	0.2138	(0.1821, 0.2483)	14.99	19922.0	422.0	1.0	1.0
GTR:sym[AC]	0.0189	±	0.01566	0.01505	(5.389e-08, 0.04966)	10.4	28725.0	424.0	1.0	1.0
GTR:sym[AG]	0.1844	±	0.03853	0.1817	(0.1114, 0.2608)	16.35	18260.0	813.0	1.001	1.0
GTR:sym[AU]	0.2735	±	0.04997	0.2715	(0.1774, 0.3717)	18.15	16456.0	616.0	0.9993	0.9998
GTR:sym[CG]	0.09195	±	0.02817	0.08941	(0.04029, 0.1487)	24.65	12114.0	637.0	1.0	1.0
GTR:sym[CU]	0.3947	±	0.05711	0.3924	(0.2843, 0.5075)	17.47	17094.0	613.0	1.0	1.0
GTR:sym[GU]	0.0366	±	0.02266	0.03373	(1.418e-06, 0.07816)	11.67	25586.0	537.0	1.0	1.0
Inv:pInv	0.1146	±	0.03659	0.1128	(0.04546, 0.1885)	5.861	50952.0	381.0	0.9993	0.9998
sigma	0.08809	±	0.1204	0.04913	(3.497e-07, 0.3287)	6.933	43069.0	231.0	0.9986	1.0
likelihood	-2703	±	13.14	-2703	(-2728, -2677)	20.67	14445.0	349.0	1.0	1.0
posterior	-3147	±	22.79	-3146	(-3193, -3104)	9.527	31344.0	290.0	0.9998	1.0
prior	-444.3	±	26.51	-442.8	(-497, -394.1)	15.38	19410.0	343.0	1.0	1.0
prior_A	-406.7	±	24.5	-405	(-455.9, -361.3)	17.47	17089.0	474.0	0.9993	1.0
scale	13.53	±	2.87	13.22	(8.378, 19.27)	6.234	47898.0	189.0	1.0	1.0
scale*\|T\|	15.73	±	2.536	15.41	(11.19, 20.78)	15.42	19365.0	487.0	0.9993	0.9999
scale1	13.53	±	2.87	13.22	(8.378, 19.27)	6.234	47898.0	189.0	1.0	1.0
scale1*\|T\|	15.73	±	2.536	15.41	(11.19, 20.78)	15.42	19365.0	487.0	0.9993	0.9999
\|A\|	163.7	±	6.24	163	(152, 175)	82.24	3631.0	686.0	1.027	1.001
\|T\|	1.19	±	0.1996	1.177	(0.8121, 1.585)	1.32	226232.0	168.0	0.9995	0.9998
\|indels\|	106.7	±	9.59	106	(89, 125)	24.44	12219.0	354.0	0.9825	1.0

Phylogeny Distribution

50% consensus tree

Partition support: Summary · Across chains

Tree files
Tree	Consensus tree
Tree	Newick	+PP	PDF	SVG
greedy	Newick	+PP	PDF	SVG
MAP	Newick	+PP	PDF	SVG
50% consensus	Newick	+PP	PDF	SVG
66% consensus	Newick	+PP	PDF	SVG
80% consensus	Newick	+PP	PDF	SVG
90% consensus	Newick	+PP	PDF	SVG
95% consensus	Newick	+PP	PDF	SVG
99% consensus	Newick	+PP	PDF	SVG
100% consensus	Newick	+PP	PDF	SVG

Consensus-tree support levels

Alignment Distribution

Partition 1

Alignment	FASTA	HTML	Difference from the WPD alignment	AU	Minimum pairwise sequence identity	Number of alignment columns	Number of invariant columns	Number of parsimony-informative columns
Initial	FASTA	HTML	Diff	AU	12.7%	131	0 (0%)	126 (96.2%)
Consensus (posterior-decoding: very short/log)	FASTA	HTML		AU	33.6%	151	11 (7.28%)	114 (75.5%)
Consensus (posterior-decoding: short/EA)	FASTA	HTML		AU	34.1%	157	11 (7.01%)	121 (77.1%)
Consensus (posterior-decoding: medium/AMA)	FASTA	HTML		AU	33.8%	170	11 (6.47%)	119 (70%)
Consensus (posterior-decoding: long/TC)	FASTA	HTML		AU	26.1%	201	11 (5.47%)	131 (65.2%)
Ancestral	FASTA	HTML			31.8%	170	11 (6.47%)	144 (84.7%)

Convergence and mixing

Statistics
scalar burnin	813
scalar ESS	3631
minimum topological ESS	2969.687
ASDSF	0.009
MSDSF	0.028
PSRF-80%CI	1.027
PSRF-RCF	1.002

SRQ plot for support of the 50% consensus tree. — 50% consensus-tree split support

SRQ plot for support of each sampled split. — All sampled splits

Projection of RF distances for the first 4 chains (Hillis et al 2005)

3D

Split posterior probabilities across chains (Beiko et al 2006)

Split posterior log odds across chains

Run details

command line: bali-phy 25.fasta --smodel 'GTR +> ASRV.Gamma(4) +> Inv +> Covarion.Huelsenbeck02'
directory: /home/bredelings/Projects/5S-25
version: 4.3

chain #	burnin	subsample	samples	subdirectory
1	3627	1	33651	25-1
2	3627	1	33630	25-2
3	3627	1	33621	25-3
4	3627	1	33526	25-4
5	3627	1	33557	25-5
6	3627	1	33417	25-6
7	3627	1	33499	25-7
8	3627	1	33257	25-8
9	3627	1	32931	25-9

Model and priors

Tree (+priors)

tree ~ UniformTree(taxa, Gamma(0.5, (1 / length(@taxa))))

subst rates = constant

indel rates = map(|x:pow(x, sigma)|, ~IIDMap(branches(tree), LogNormal(0, 1))) where {sigma ~ LogLaplace((-3), 1)}

Substitution model (+priors)

S1

= GTR +> ASRV.Gamma(n=4) +> Inv +> Covarion.Huelsenbeck02

GTR:sym ~ SymmetricDirichletOn(letter_pairs(@a), 1)

GTR:pi ~ SymmetricDirichletOn(letters(@a), 1)

ASRV.Gamma:alpha ~ LogLaplace(6, 2)

Inv:pInv ~ Uniform(0, 1)

Covarion.Huelsenbeck02:r ~ Gamma(2, (1 / 4))

Covarion.Huelsenbeck02:pi1 ~ Beta(2, 2)

Indel model (+priors)

I1

= RS07

RS07:rate ~ LogLaplace((-4), 0.707)

RS07:meanLength ~ ShiftedExponential(10, 1)

Scales (+priors)

scale1 ~ Gamma(0.5, 2)

Model Code

BAliPhy.Main.hs

Glossary

ACT: Autocorrelation time measures serial dependence. The effective sample size is the retained sample count divided by ACT.
ESS: Effective sample size approximates the number of independent samples that would give the same precision as the correlated MCMC samples. Values below 100 are flagged as concerning, and values from 100 through 299 warrant caution; obtaining more samples should increase ESS.
PSRF-80%CI: The width of the pooled 80% credible interval divided by the average within-chain width. Values from 1.05 through 1.19 warrant caution, and values of 1.2 or greater are concerning. Values near 1 indicate similar widths across chains.
PSRF-RCF: For each chain's 80% credible interval, this compares its probability in that chain with its probability in the pooled samples, then averages the ratios across chains. It uses the same warning thresholds as PSRF-80%CI.
ASDSF: The average across splits of the standard deviation, across chains, of each split's posterior probability. Values below 0.01 are commonly considered acceptable; larger values suggest obtaining more samples or comparing additional chains.
MSDSF: The largest standard deviation across chains of any split's posterior probability. A large value identifies at least one split whose estimated support still differs substantially among chains.