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。

99.scripts/workflow/orthology_inference/02.trim_alignment.sh

@@ -0,0 +1,20 @@
+#! /bin/bash
+set -e
+THREADS=${THREADS:-12}
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <nal_dir> <out_dir> <ext>"
+    echo "Trim MACSE nucleotide alignments using trimal"
+    exit 1
+fi
+
+nal_dir=$(readlink -f "$1")
+out_dir=$(readlink -f "$2")
+ext=$3
+
+mkdir -p "$out_dir"
+echo -n >trimal.cmds
+for i in "$nal_dir"/*."$ext"; do
+    j=$(basename "$i" ."$ext")
+    echo "trimal -in $i -out $out_dir/${j}.trimed.fa -automated1 -resoverlap 0.5 -seqoverlap 50" >>trimal.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a trimal.cmds bash -c "cmd"