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.

This commit is contained in:

agent

2025-12-20 23:33:05 +08:00

parent dba4833905

commit e467d67723

16 changed files with 353 additions and 1265 deletions

.gitignore

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