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/01.macse_align.sh

@@ -0,0 +1,24 @@
+#! /bin/bash
+set -e
+THREADS=${THREADS:-12}
+EXT=${EXT:-"fa"}
+
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <ogs_dir> <out_dir>"
+    echo "Perform MACSE alignment for each orthologous group"
+    exit 1
+fi
+
+ogs_dir=$(readlink -f "$1")
+out_dir=$2
+
+mkdir -p "$out_dir"
+echo "Starting MACSE alignment of orthologous groups..."
+echo -n >macse.cmds
+for og_fasta in "$ogs_dir"/*."$EXT"; do
+    og_name=$(basename "$og_fasta" ."$EXT")
+    out_stem="$out_dir/$og_name"
+    echo "macse -prog alignSequences -seq $og_fasta -out_AA ${out_stem}.pal -out_NT ${out_stem}.nal > ${out_stem}.log 2>&1" >>macse.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a macse.cmds bash -c "cmd" &&
+    echo "MACSE alignment completed."