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.

99.scripts/workflow/orthology_inference/04.filter_ogs.sh

@@ -0,0 +1,23 @@
+#! /bin/bash
+set -e
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <out_dir> <treeshrink_dir> <min_taxon> <min_seq_length>"
+    echo "Filter orthologous groups after TreeShrink based on minimum taxon number and minimum sequence length"
+    exit 1
+fi
+
+out_dir=$(readlink -f "$1")
+treeshrink_dir=$(readlink -f "$2")
+min_taxon=$3
+min_seq_length=$4
+
+mkdir -p "$out_dir"
+for i in "$treeshrink_dir"/*/output.fasta; do
+    j=$(dirname "$i")
+    j=$(basename "$j")
+    seqlen=$(seqkit fx2tab -C ATCG "$i" | awk '{print $3}' | sort -n | head -n 1)
+    seqnum=$(grep -c ">" "$i")
+    if [[ $seqnum -eq $min_taxon && $seqlen -ge $min_seq_length ]]; then
+        cp -l "$i" "$out_dir"/"${j}.fa"
+    fi
+done

99.scripts/workflow/orthology_inference/09.filter_ogs.sh

@@ -1,12 +0,0 @@
-#! /usr/bin/env bash
-total_taxon=11
-min_seq_length=300
-mkdir -p final_ogs
-for i in treeshrink/* ; do
-    j=$(basename "$i")
-    seqlen=$(seqkit fx2tab -C ATCG "$i"/output.fasta | awk '{print $3}' | sort -n | head -n 1)
-    seqnum=$(grep -c ">" "$i"/output.fasta)
-    if [[ $seqnum -eq $total_taxon && $seqlen -ge $min_seq_length ]]; then
-        cp -l "$i"/output.fasta final_ogs/"${j}.fa"
-    fi
-done