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.

.gitignore

@@ -10,6 +10,7 @@
 05.reduce_redundancy/*
 05.orthology_inference/*
 06.phylogeny_reconstruction/*
+06.phylogenetic_analysis/*
 06.gene_trees/*
 10.plastid/*
 98.results/*

99.scripts/miscs/mrbayes.sh

@@ -0,0 +1,20 @@
+#! /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

@@ -0,0 +1,20 @@
+#! /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

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

99.scripts/workflow/phylogeny_reconstruction/01.modeltest.sh

@@ -1,7 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p modeltests
-for i in ../gene_alignment/*.fa ; do
-    j=$(basename "$i")
-    echo "modeltest-ng -p 2 -r 12345 --force -i $i -d nt -t ml -o modeltests/${j/.fa/}.modeltest" >> modeltest.cmds
-done
-xargs -t -P 4 -I cmd -a modeltest.cmds bash -c "cmd"

99.scripts/workflow/phylogeny_reconstruction/01.run_mrbayes.sh

@@ -0,0 +1,21 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <input_fasta_dir> <extension> <output_dir>"
+    echo "Run MrBayes for each fasta file in the input directory"
+    exit 1
+fi
+
+input_dir=$(readlink -f "$1")
+ext=$2
+output_dir=$(readlink -f "$3")
+mkdir -p "${output_dir}"
+echo -n >mrbayes.cmds
+for f in "${input_dir}"/*."${ext}"; do
+    j=$(basename "$f" ."${ext}")
+    echo "bash $SCRIPTS/miscs/mrbayes.sh $f ${output_dir}/${j}/${j}.nex" >>mrbayes.cmds
+done
+xargs -t -P 12 -I cmd -a mrbayes.cmds bash -c "cmd"
+echo "All MrBayes analyses are done!"

99.scripts/workflow/phylogeny_reconstruction/02.mbsum.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+THREADS=${THREADS:-12}
+MIN_DSF=${MIN_DSF:-0.01}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <mrbayes_output_dir> <mbsum_output_dir> <num_skip>"
+    echo "Summarize MrBayes output using mbsum, skipping analyses with high DSF"
+    exit 1
+fi
+
+mb_dir=$(readlink -f "$1")
+mbsum_out_dir=$2
+num_skip=$3
+
+mkdir -p "$mbsum_out_dir"
+echo -n "" >mbsum.skip.log
+echo -n "" >mbsum.cmds
+for i in "$mb_dir"/*/mrbayes.log; do
+    og_dir=$(dirname "$i")
+    base=$(basename "$og_dir")
+    ## skip Average standard deviation of split frequencies > 0.01
+    dsf=$(awk '/Average standard deviation of split frequencies:/ {out=$7} END{print out+0}' "$i" 2>/dev/null)
+    if awk -v d="$dsf" -v min_dsf="$MIN_DSF" 'BEGIN{if (d >= min_dsf) exit 0; exit 1}'; then
+        echo "Skipping ${base} due to high DSF: ${dsf}" >>mbsum.skip.log
+        continue
+    else
+        echo "mbsum ${og_dir}/*.t -n $num_skip -o $mbsum_out_dir/${base}.in >> $og_dir/mbsum.log 2>&1" >>mbsum.cmds
+    fi
+done
+xargs -t -P "$THREADS" -I cmd -a mbsum.cmds bash -c "cmd"
+echo "Mbsum all done!"

99.scripts/workflow/phylogeny_reconstruction/02.raxml_per_gene.sh

@@ -1,9 +0,0 @@
-#! /usr/bin/env bash
-mkdir -p raxml_ng
-echo -n > raxml_ng.cmds
-for i in modeltests/*.modeltest.out ; do
-    j=$(basename "$i")
-    cmd=$(grep "raxml-ng" "$i" | tail -n 1 | sed 's/> //')
-    echo "$cmd --all --bs-trees 1000 --outgroup Zju --redo --threads 4 --seed 12345 --prefix raxml_ng/${j/.modeltest.out/} > /dev/null" >> raxml_ng.cmds
-done
-xargs -t -P 3 -I cmd -a raxml_ng.cmds bash -c "cmd"

99.scripts/workflow/phylogeny_reconstruction/03.run_raxml.sh

@@ -0,0 +1,23 @@
+#! /bin/bash
+set -e
+SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
+THREADS=${THREADS:-4}
+
+if [ "$#" -ne 3 ]; then
+    echo "Usage: $0 <in_dir> <out_dir> <ext>"
+    echo "Run raxml-ng on filtered orthogroup alignments"
+    exit 1
+fi
+
+in_dir=$(readlink -f "$1")
+out_dir=$2
+ext=$3
+mkdir -p "$out_dir"
+echo -n >raxml.cmds
+for i in "$in_dir"/*."$ext"; do
+    j=$(basename "$i" ."$ext")
+    out_prefix="$out_dir/${j}/${j}"
+    echo "$SCRIPTS/miscs/raxml.sh $i $out_prefix 4 Zju" >>raxml.cmds
+done
+xargs -t -P "$THREADS" -I cmd -a raxml.cmds bash -c "cmd"
+echo "Raxml-ng all completed."

99.scripts/workflow/phylogeny_reconstruction/07.mbsum.sh

@@ -1,21 +0,0 @@
-#!/usr/bin/env bash
-
-mkdir -p ../mbsum_out
-echo -n "" > ../mbsum.log
-for i in *.nex.tar.gz; do
-    base=$(basename "$i" .nex.tar.gz)
-    echo "Processing ${base}" >> ../mbsum.log
-    mkdir -p "${base}"
-    tar -xzf "$i" -C "${base}"
-    ## skip Average standard deviation of split frequencies > 0.01
-    dsf=$(awk '/Average standard deviation of split frequencies:/ {out=$7} END{print out+0}' "${base}"/*.nex.log 2>/dev/null)
-    if awk -v d="$dsf" 'BEGIN{if (d >= 0.01) exit 0; exit 1}'; then
-        echo "Skipping ${base} due to high DSF: ${dsf}" >> ../mbsum.log
-        continue
-    else
-        mbsum "${base}"/*.t -n 1000 -o ../mbsum_out/"${base}".in >> ../mbsum.log 2>&1
-    fi
-    rm -rf "${base}"
-    echo "Completed ${base}" >> ../mbsum.log
-done
-echo "All done!"

pixi.lock

@@ -1,5 +1,78 @@
 version: 6
 environments:
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+    - url: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
+    - url: https://conda.anaconda.org/conda-forge/
+    - url: https://conda.anaconda.org/bioconda/
+    packages:
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   default:
     channels:
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@@ -22,8 +95,7 @@ environments:
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-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/beast-10.5.0-hdfd78af_0.tar.bz2
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@@ -239,6 +311,7 @@ environments:
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       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libllvm21-21.1.0-hecd9e04_0.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libltdl-2.4.3a-h5888daf_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/liblzma-devel-5.8.1-hb9d3cd8_2.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libmamba-2.3.2-hae34dd5_2.conda
@@ -272,6 +345,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libsuitesparseconfig-7.10.1-h901830b_7100101.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libsystemd0-257.10-hd0affe5_2.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libtiff-4.7.1-h9d88235_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libtool-2.5.4-h5888daf_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libtorch-2.6.0-cpu_generic_haed06de_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libumfpack-6.3.5-h873dde6_7100101.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libunistring-0.9.10-h7f98852_0.tar.bz2
@@ -312,6 +386,7 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/mpg123-1.32.9-hc50e24c_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/mpi-1.0-openmpi.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/mpmath-1.3.0-pyhd8ed1ab_1.conda
+      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/mrbayes-3.2.7-hd0d793b_7.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/munkres-1.1.4-pyhd8ed1ab_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/muscle-3.8.1551-h9948957_9.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/mysql-connector-c-6.1.11-h659d440_1008.conda
@@ -337,7 +412,6 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/ossuuid-1.6.2-h5888daf_1001.conda
       - 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
@@ -370,7 +444,6 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-file-path-2.18-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-file-temp-0.2304-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-file-which-1.24-pl5321hd8ed1ab_0.tar.bz2
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/perl-getopt-long-2.58-pl5321hdfd78af_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-importer-0.026-pl5321hd8ed1ab_0.tar.bz2
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/perl-inc-latest-0.500-pl5321ha770c72_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/linux-64/perl-io-compress-2.213-pl5321h503566f_0.conda
@@ -728,88 +801,6 @@ environments:
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zlib-ng-2.2.5-hde8ca8f_0.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstandard-0.25.0-py311haee01d2_1.conda
       - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
-  mrbayes:
-    channels:
-    - url: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
-    - url: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/
-    - url: https://conda.anaconda.org/conda-forge/
-    - url: https://conda.anaconda.org/bioconda/
-    packages:
-      linux-64:
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/alsa-lib-1.2.14-hb9d3cd8_0.conda
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-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/ca-certificates-2025.11.12-hbd8a1cb_0.conda
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/cairo-1.18.4-h3394656_0.conda
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-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2
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-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda
-      - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
 packages:
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
   sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726
@@ -846,6 +837,16 @@ packages:
   license_family: GPL
   size: 566531
   timestamp: 1744668655747
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/alsa-lib-1.2.15.1-hb03c661_0.conda
+  sha256: 224f1a55a9ba7e877bce980f14fc3e3c0f0fb6d3cbf3c5f1a8f5dd8391ce8bba
+  md5: bba37fb066adb90e1d876dff0fd5d09d
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  license: LGPL-2.1-or-later
+  license_family: GPL
+  size: 585491
+  timestamp: 1766155792553
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/aom-3.9.1-hac33072_0.conda
   sha256: b08ef033817b5f9f76ce62dfcac7694e7b6b4006420372de22494503decac855
   md5: 346722a0be40f6edc53f12640d301338
@@ -3515,6 +3516,18 @@ packages:
   license_family: MIT
   size: 74811
   timestamp: 1752719572741
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libexpat-2.7.3-hecca717_0.conda
+  sha256: 1e1b08f6211629cbc2efe7a5bca5953f8f6b3cae0eeb04ca4dacee1bd4e2db2f
+  md5: 8b09ae86839581147ef2e5c5e229d164
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  constrains:
+  - expat 2.7.3.*
+  license: MIT
+  license_family: MIT
+  size: 76643
+  timestamp: 1763549731408
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libffi-3.5.2-h9ec8514_0.conda
   sha256: 25cbdfa65580cfab1b8d15ee90b4c9f1e0d72128f1661449c9a999d341377d54
   md5: 35f29eec58405aaf55e01cb470d8c26a
@@ -3572,6 +3585,19 @@ packages:
   license_family: GPL
   size: 822552
   timestamp: 1759968052178
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgcc-15.2.0-he0feb66_16.conda
+  sha256: 6eed58051c2e12b804d53ceff5994a350c61baf117ec83f5f10c953a3f311451
+  md5: 6d0363467e6ed84f11435eb309f2ff06
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - _openmp_mutex >=4.5
+  constrains:
+  - libgcc-ng ==15.2.0=*_16
+  - libgomp 15.2.0 he0feb66_16
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 1042798
+  timestamp: 1765256792743
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/libgcc-devel_linux-64-15.2.0-h73f6952_107.conda
   sha256: 67323768cddb87e744d0e593f92445cd10005e04259acd3e948c7ba3bcb03aed
   md5: 85fce551e54a1e81b69f9ffb3ade6aee
@@ -3581,6 +3607,15 @@ packages:
   license_family: GPL
   size: 2728965
   timestamp: 1759967882886
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_16.conda
+  sha256: 5f07f9317f596a201cc6e095e5fc92621afca64829785e483738d935f8cab361
+  md5: 5a68259fac2da8f2ee6f7bfe49c9eb8b
+  depends:
+  - libgcc 15.2.0 he0feb66_16
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 27256
+  timestamp: 1765256804124
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgcc-ng-15.2.0-h69a702a_7.conda
   sha256: 2045066dd8e6e58aaf5ae2b722fb6dfdbb57c862b5f34ac7bfb58c40ef39b6ad
   md5: 280ea6eee9e2ddefde25ff799c4f0363
@@ -3686,6 +3721,21 @@ packages:
   license: LGPL-2.1-or-later
   size: 3933707
   timestamp: 1762787455198
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libglib-2.86.3-h6548e54_0.conda
+  sha256: 82d6c2ee9f548c84220fb30fb1b231c64a53561d6e485447394f0a0eeeffe0e6
+  md5: 034bea55a4feef51c98e8449938e9cee
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libffi >=3.5.2,<3.6.0a0
+  - libgcc >=14
+  - libiconv >=1.18,<2.0a0
+  - libzlib >=1.3.1,<2.0a0
+  - pcre2 >=10.47,<10.48.0a0
+  constrains:
+  - glib 2.86.3 *_0
+  license: LGPL-2.1-or-later
+  size: 3946542
+  timestamp: 1765221858705
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libglvnd-1.7.0-ha4b6fd6_2.conda
   sha256: 1175f8a7a0c68b7f81962699751bb6574e6f07db4c9f72825f978e3016f46850
   md5: 434ca7e50e40f4918ab701e3facd59a0
@@ -3713,6 +3763,15 @@ packages:
   license_family: GPL
   size: 447919
   timestamp: 1759967942498
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libgomp-15.2.0-he0feb66_16.conda
+  sha256: 5b3e5e4e9270ecfcd48f47e3a68f037f5ab0f529ccb223e8e5d5ac75a58fc687
+  md5: 26c46f90d0e727e95c6c9498a33a09f3
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 603284
+  timestamp: 1765256703881
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libheif-1.19.7-gpl_hc18d805_100.conda
   sha256: ec9797d57088aeed7ca4905777d4f3e70a4dbe90853590eef7006b0ab337af3f
   md5: 1db2693fa6a50bef58da2df97c5204cb
@@ -4092,6 +4151,16 @@ packages:
   license: zlib-acknowledgement
   size: 317390
   timestamp: 1753879899951
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libpng-1.6.53-h421ea60_0.conda
+  sha256: 8acdeb9a7e3d2630176ba8e947caf6bf4985a5148dec69b801e5eb797856688b
+  md5: 00d4e66b1f746cb14944cad23fffb405
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  - libzlib >=1.3.1,<2.0a0
+  license: zlib-acknowledgement
+  size: 317748
+  timestamp: 1764981060755
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libpq-17.6-h3675c94_2.conda
   sha256: 8a078b33f65c5521ae1ed9545ea21efdc46630ff618cdd01aa6a3e698149b27d
   md5: e2c2f4c4c20a449b3b4a218797bd7c03
@@ -4236,6 +4305,18 @@ packages:
   license_family: GPL
   size: 3898269
   timestamp: 1759968103436
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libstdcxx-15.2.0-h934c35e_16.conda
+  sha256: 813427918316a00c904723f1dfc3da1bbc1974c5cfe1ed1e704c6f4e0798cbc6
+  md5: 68f68355000ec3f1d6f26ea13e8f525f
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc 15.2.0 he0feb66_16
+  constrains:
+  - libstdcxx-ng ==15.2.0=*_16
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 5856456
+  timestamp: 1765256838573
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/libstdcxx-devel_linux-64-15.2.0-h73f6952_107.conda
   sha256: ae5f609b3df4f4c3de81379958898cae2d9fc5d633518747c01d148605525146
   md5: a888a479d58f814ee9355524cc94edf3
@@ -4254,6 +4335,15 @@ packages:
   license_family: GPL
   size: 29343
   timestamp: 1759968157195
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libstdcxx-ng-15.2.0-hdf11a46_16.conda
+  sha256: 81f2f246c7533b41c5e0c274172d607829019621c4a0823b5c0b4a8c7028ee84
+  md5: 1b3152694d236cf233b76b8c56bf0eae
+  depends:
+  - libstdcxx 15.2.0 h934c35e_16
+  license: GPL-3.0-only WITH GCC-exception-3.1
+  license_family: GPL
+  size: 27300
+  timestamp: 1765256885128
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libsuitesparseconfig-7.10.1-h901830b_7100101.conda
   sha256: d8f32a0b0ee17fbace7af4bd34ad554cc855b9c18e0aeccf8395e1478c161f37
   md5: 57ae1dd979da7aa88a9b38bfa2e1d6b2
@@ -4374,6 +4464,16 @@ packages:
   license_family: MIT
   size: 85741
   timestamp: 1757742873826
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libuuid-2.41.2-h5347b49_1.conda
+  sha256: 030447cf827c471abd37092ab9714fde82b8222106f22fde94bc7a64e2704c40
+  md5: 41f5c09a211985c3ce642d60721e7c3e
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libgcc >=14
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 40235
+  timestamp: 1764790744114
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/libuuid-2.41.2-he9a06e4_0.conda
   sha256: e5ec6d2ad7eef538ddcb9ea62ad4346fde70a4736342c4ad87bd713641eb9808
   md5: 80c07c68d2f6870250959dcc95b209d1
@@ -5116,16 +5216,6 @@ packages:
   license_family: APACHE
   size: 62477
   timestamp: 1745345660407
-- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/pal2nal-14.1-pl5321hdfd78af_3.tar.bz2
-  sha256: aff933ffefe2ecbc31b6e38bbbb2a19b5b34c2942b3d2078d7f5848432d494f6
-  md5: 2afdf27b9f28038bfb670e2059deca04
-  depends:
-  - perl >=5.32.1,<6.0a0 *_perl5
-  - perl-getopt-long
-  license: GPLv2.0
-  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
@@ -5260,6 +5350,18 @@ packages:
   license_family: BSD
   size: 1209177
   timestamp: 1756742976157
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/pcre2-10.47-haa7fec5_0.conda
+  sha256: 5e6f7d161356fefd981948bea5139c5aa0436767751a6930cb1ca801ebb113ff
+  md5: 7a3bff861a6583f1889021facefc08b1
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - bzip2 >=1.0.8,<2.0a0
+  - libgcc >=14
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 1222481
+  timestamp: 1763655398280
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.conda
   build_number: 7
   sha256: 9ec32b6936b0e37bcb0ed34f22ec3116e75b3c0964f9f50ecea5f58734ed6ce9
@@ -5515,14 +5617,6 @@ packages:
   license_family: OTHER
   size: 17329
   timestamp: 1636695979827
-- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda/noarch/perl-getopt-long-2.58-pl5321hdfd78af_0.tar.bz2
-  sha256: 94c17b270316f9b38cf1afa0b1724cdb6bd8349207568dccc1156b9014708c7d
-  md5: 10469a3defbd6dbab17d3d10dd6fd828
-  depends:
-  - perl >=5.32.1,<6.0a0 *_perl5
-  license: unknown
-  size: 33785
-  timestamp: 1718113256479
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/noarch/perl-importer-0.026-pl5321hd8ed1ab_0.tar.bz2
   sha256: f40d5302de8c81282b5216edd8c65aecc551ef725db3351c208bff9b077e66a2
   md5: 66e17c342d13c39a12c1059f13f9b72c
@@ -10260,6 +10354,16 @@ packages:
   license: BSD-3-Clause
   size: 466893
   timestamp: 1762512695614
+- conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda
+  sha256: 68f0206ca6e98fea941e5717cec780ed2873ffabc0e1ed34428c061e2c6268c7
+  md5: 4a13eeac0b5c8e5b8ab496e6c4ddd829
+  depends:
+  - __glibc >=2.17,<3.0.a0
+  - libzlib >=1.3.1,<2.0a0
+  license: BSD-3-Clause
+  license_family: BSD
+  size: 601375
+  timestamp: 1764777111296
 - conda: https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda
   sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb
   md5: 6432cb5d4ac0046c3ac0a8a0f95842f9

pixi.toml

@@ -15,8 +15,6 @@ index-url = "https://mirrors.bfsu.edu.cn/pypi/web/simple"
 
 [tasks]
 
-[dependencies]
-
 [feature.base.dependencies]
 sra-tools = "*"
 fastp = "*"
@@ -31,20 +29,17 @@ pip = ">=25.2,<26"
 seqkit = ">=2.10.1,<3"
 r-rstan = ">=2.32.7,<3"
 biopython = ">=1.85,<2"
-pal2nal = ">=14.1,<15"
 trimal = ">=1.5.0,<2"
 treeshrink = ">=1.3.9,<2"
 r-ape = ">=5.8_1,<6"
 raxml-ng = ">=1.2.2,<2"
 modeltest-ng = ">=0.1.7,<0.2"
-beast = ">=10.5.0,<11"
 aster = ">=1.23,<2"
 julia = "1.12.*"
 conda = ">=25.9.1,<26"
 r-phangorn = ">=2.12.1,<3"
 r-languageserver = ">=0.3.16,<0.4"
 seqmagick = ">=0.8.6,<0.9"
-beagle-lib = "4.*"
 maven = ">=3.9.11,<4"
 matplotlib = ">=3.10.8,<4"
 ete3 = ">=3.1.3,<4"
@@ -54,12 +49,13 @@ macse = ">=2.7,<3"
 td2 = ">=1.0.6,<2"
 mmseqs2 = ">=18.8cc5c,<19"
 paml = ">=4.10.9,<5"
+beagle-lib = "==3.1.2"
+mrbayes = ">=3.2.7,<4"
 
-[feature.mrbayes.dependencies]
-beagle-lib = ">=3.1.2,<4"
-mrbayes = ">=3.2.7"
+[feature.beast.dependencies]
+beagle-lib = ">=4.0.1,<5"
+beast = ">=10.5.0,<11"
 
 [environments]
 default = ["base"]
-mrbayes = ["mrbayes"]
-
+beast = ["beast"]