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
parent e8ba2ed962
commit dba4833905
15 changed files with 433 additions and 117 deletions
@@ -29,7 +29,6 @@ cd-hit = ">=4.8.1,<5"
 orthofinder = ">=3.1.0,<4"
 pip = ">=25.2,<26"
 seqkit = ">=2.10.1,<3"
-hmmer = ">=3.4,<4"
 r-rstan = ">=2.32.7,<3"
 biopython = ">=1.85,<2"
 pal2nal = ">=14.1,<15"
@@ -54,6 +53,7 @@ r-ggplot2 = ">=4.0.1,<5"
 macse = ">=2.7,<3"
 td2 = ">=1.0.6,<2"
 mmseqs2 = ">=18.8cc5c,<19"
+paml = ">=4.10.9,<5"

 [feature.mrbayes.dependencies]
 beagle-lib = ">=3.1.2,<4"