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.
23 lines
389 B
Plaintext
23 lines
389 B
Plaintext
# pixi environments
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.pixi/*
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!.pixi/config.toml
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.pueue/*
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00.rawdata/*
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01.reference/*
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02.mapping_assembly/*
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03.denovo_assembly/*
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04.cds_prediction/*
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05.reduce_redundancy/*
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05.orthology_inference/*
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06.phylogeny_reconstruction/*
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06.phylogenetic_analysis/*
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06.gene_trees/*
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10.plastid/*
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98.results/*
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99.scripts/bucky/
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99.scripts/phyparts/
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99.scripts/bpp/
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run.status.json
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!*/_description.md
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tmp/
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