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IvisTang e467d67723 Add scripts for phylogenetic analysis using MrBayes and RAxML 
- Created `mbblock.txt` for MrBayes configuration.
- Implemented `mrbayes.sh` to convert FASTA to Nexus and run MrBayes.
- Developed `raxml.sh` to run modeltest-ng and raxml-ng on alignments.
- Added `04.filter_ogs.sh` to filter orthologous groups based on taxon count and sequence length.
- Implemented `01.run_mrbayes.sh` to execute MrBayes for multiple FASTA files.
- Created `02.mbsum.sh` to summarize MrBayes output while skipping high DSF analyses.
- Developed `03.run_raxml.sh` to run raxml-ng on filtered alignments.
 		2025-12-20 23:33:05 +08:00
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__pycache__ 20251125 2025-11-25 00:28:51 +08:00
plastid 20251125 2025-11-25 00:28:51 +08:00
bucky.pl Add scripts for phylogenetic analysis using MrBayes and RAxML 2025-12-20 23:33:05 +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
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 Add scripts for phylogenetic analysis using MrBayes and RAxML 2025-12-20 23:33:05 +08:00
rename_trinity_fasta.py Add Vercel configuration for rewrites and build settings 2025-12-17 17:47:45 +08:00