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biyelunwen/99.scripts/miscs
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IvisTang 7f4e888e6a 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.
 		2026-01-18 13:26:16 +08:00
..
__pycache__ 20251125 2025-11-25 00:28:51 +08:00
plastid 20251125 2025-11-25 00:28:51 +08:00
bucky.pl 更新脚本和配置，修复 BUCKy 版本检查逻辑，调整 RAxML 脚本参数，增加 cairosvg 依赖，并更新 pixi.lock 文件以反映新依赖。 2025-12-24 09:00:15 +08:00
check_and_translate_outgroup_cds.py 20251125 2025-11-25 00:28:51 +08:00
check_frameshift.py 更新 .gitignore，添加 06.gene_trees 目录；重构 macse.sh 脚本，移除 fs_lr 参数；删除多个不再使用的脚本；添加 check_frameshift.py 和 get_og_seqs.py 脚本以处理阅读框移位和提取单拷贝OG序列；更新 pixi.toml 和 pixi.lock 文件以添加 paml 依赖。 2025-12-20 01:57:25 +08:00
get_og_seqs.py 更新 .gitignore，添加 06.gene_trees 目录；重构 macse.sh 脚本，移除 fs_lr 参数；删除多个不再使用的脚本；添加 check_frameshift.py 和 get_og_seqs.py 脚本以处理阅读框移位和提取单拷贝OG序列；更新 pixi.toml 和 pixi.lock 文件以添加 paml 依赖。 2025-12-20 01:57:25 +08:00
get_primary_cds.py 更新 .gitignore，添加 06.gene_trees 目录；重构 macse.sh 脚本，移除 fs_lr 参数；删除多个不再使用的脚本；添加 check_frameshift.py 和 get_og_seqs.py 脚本以处理阅读框移位和提取单拷贝OG序列；更新 pixi.toml 和 pixi.lock 文件以添加 paml 依赖。 2025-12-20 01:57:25 +08:00
hmmsearch_result_to_new_ogs_dir.py Add Vercel configuration for rewrites and build settings 2025-12-17 17:47:45 +08:00
macse.sh 更新 .gitignore，添加 06.gene_trees 目录；重构 macse.sh 脚本，移除 fs_lr 参数；删除多个不再使用的脚本；添加 check_frameshift.py 和 get_og_seqs.py 脚本以处理阅读框移位和提取单拷贝OG序列；更新 pixi.toml 和 pixi.lock 文件以添加 paml 依赖。 2025-12-20 01:57:25 +08:00
mbblock.txt Add scripts for phylogenetic analysis using MrBayes and RAxML 2025-12-20 23:33:05 +08:00
mcmctree.ctl Add MCMCtree workflow and SNaQ analysis scripts 2026-01-18 13:26:16 +08:00
mcmctree_workflow.r Add MCMCtree workflow and SNaQ analysis scripts 2026-01-18 13:26:16 +08:00
mrbayes.sh Add scripts for phylogenetic analysis using MrBayes and RAxML 2025-12-20 23:33:05 +08:00
ogs_list_to_ogs_fasta.py 20251125 2025-11-25 00:28:51 +08:00
phypartspiecharts.py 20251125 2025-11-25 00:28:51 +08:00
raxml.sh 更新脚本和配置，修复 BUCKy 版本检查逻辑，调整 RAxML 脚本参数，增加 cairosvg 依赖，并更新 pixi.lock 文件以反映新依赖。 2025-12-24 09:00:15 +08:00
rename_trinity_fasta.py Add Vercel configuration for rewrites and build settings 2025-12-17 17:47:45 +08:00