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。

pixi.lock

@@ -338,6 +338,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/p7zip-16.02-h9c3ff4c_1001.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/pal2nal-14.1-pl5321hdfd78af_3.tar.bz2
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/paml-4.10.9-h7b50bb2_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pandas-2.3.3-py311hed34c8f_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pandoc-3.8.2.1-ha770c72_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pango-1.56.4-hadf4263_0.conda
@@ -5125,6 +5126,15 @@ packages:
   license_family: GPL
   size: 22693
   timestamp: 1642293349880
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/paml-4.10.9-h7b50bb2_1.conda
+  sha256: 81c5237b07796984d7915d29a768068a1e5e6c02b4ae25f27836b0babe84e5aa
+  md5: ef02b401c5daaf104b3d1091f8ec37f5
+  depends:
+  - libgcc >=13
+  license: GPL-3.0-or-later
+  license_family: GPL3
+  size: 679359
+  timestamp: 1755706728619
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pandas-2.3.3-py311hed34c8f_1.conda
   sha256: c97f796345f5b9756e4404bbb4ee049afd5ea1762be6ee37ce99162cbee3b1d3
   md5: 72e3452bf0ff08132e86de0272f2fbb0