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.

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"]