agent
7f4e888e6a
- Updated `pixi.toml` to include new R package dependencies for MCMCtree workflow. - Modified markdown file to remove unnecessary simulation data discussion. - Introduced `.lintr` configuration for linting R scripts. - Created `mcmctree.ctl` control file for MCMCtree analysis. - Developed `mcmctree_workflow.r` script to orchestrate MCMCtree analysis with model testing and ESS checks. - Added `06.snaq.jl` script for SNaQ analysis with plotting capabilities. - Implemented `07.mcmctree.sh` bash script to run MCMCtree on multiple alignments in parallel.
33 lines
1.3 KiB
Plaintext
33 lines
1.3 KiB
Plaintext
seed = 12345
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seqfile = input.fa
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treefile = input.tre
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outfile = {{PREFIX_PLACEHOLDER}}.mcmctree.out
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ndata = 1
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seqtype = 0 * 0: nucleotides; 1:codons; 2:AAs
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usedata = 1 * 0: no data; 1:seq like; 2:use in.BV; 3: out.BV
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clock = 3 * 1: global clock; 2: independent rates; 3: correlated rates
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RootAge = <100 * safe constraint on root age, used if no fossil for root.
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model = {{MODEL_PLACEHOLDER}} * 0:JC69, 1:K80, 2:F81, 3:F84, 4:HKY85
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alpha = {{GAMMA_PLACEHOLDER}} * alpha for gamma rates at sites
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ncatG = 4 * No. categories in discrete gamma
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cleandata = 0 * remove sites with ambiguity data (1:yes, 0:no)?
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BDparas = 1 1 0.1 C * birth, death, sampling
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kappa_gamma = 6 2 * gamma prior for kappa
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alpha_gamma = 1 1 * gamma prior for alpha
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rgene_gamma = 2 2 * gamma prior for overall rates for genes
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sigma2_gamma = 1 10 * gamma prior for sigma^2 (for clock=2 or 3)
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finetune = 1: 0.1 0.1 0.1 0.01 .5 * auto (0 or 1) : times, musigma2, rates, mixing, paras, FossilErr
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print = 2
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burnin = 200000
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sampfreq = 200
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nsample = 5000
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*** Note: Make your window wider (100 columns) before running the program.
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