Add MCMCtree workflow and SNaQ analysis scripts

- 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.

This commit is contained in:

agent

2026-01-18 13:26:16 +08:00

parent 316017a575

commit 7f4e888e6a

11 changed files with 1068 additions and 23 deletions

.gitignore

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@@ -16,6 +16,7 @@
 .results/*
 .scripts/bucky/
 .scripts/phyparts/
 .scripts/bpp/
 run.status.json
 !*/_description.md
 tmp/