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/miscs/mbblock.txt

@@ -0,0 +1,12 @@
+begin mrbayes;
+set nowarnings=yes;
+set usebeagle=yes;
+set autoclose=yes;
+set seed=12345;
+set swapseed=12345;
+lset nst=6 rates=gamma;
+mcmcp ngen=2000000 burninfrac=.25 samplefreq=1000 printfreq=10000 checkpoint=no
+diagnfreq=10000 nruns=3 nchains=3 temp=0.40 swapfreq=10 stoprule=no;
+mcmc;
+sumt;
+end;

99.scripts/miscs/mrbayes.sh

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+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 2 ]; then
+    echo "Usage: $0 <input_fasta> <output_nexus>"
+    exit 1
+fi
+
+in_fasta=$(readlink -f "$1")
+out_nex=$2
+
+# Convert fasta to nexus
+out_dir=$(dirname "$out_nex")
+mkdir -p "$out_dir"
+seqmagick convert --output-format nexus --alphabet dna --input-format fasta "$in_fasta" "$out_nex"
+# append MrBayes block to nexus file
+cat "$SCRIPTS"/miscs/mbblock.txt >>"$out_nex"
+# Run MrBayes
+mb "$out_nex" >"${out_dir}"/mrbayes.log 2>&1

99.scripts/miscs/raxml.sh

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+#! /bin/bash
+set -e
+if [ "$#" -ne 4 ]; then
+    echo "Usage: $0 <alignment.fa> <output_prefix> <threads> <outgroup>"
+    echo "Run modeltest-ng and raxml-ng on a given alignment"
+    exit 1
+fi
+
+aln=$(readlink -f "$1")
+out=$2
+threads=$3
+outgroup=$4
+outdir=$(dirname "$out")
+mkdir -p "$outdir"
+# run modeltest-ng
+modeltest-ng -p "$threads" -r 12345 --force -i "$aln" -d nt -t ml -o "$out".modeltest
+# run raxml-ng
+cmd=$(grep "raxml-ng" "$out".modeltest.out | tail -n 1 | sed 's/> //')
+params="--all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
+bash -c "$cmd $params" >/dev/null