{"id":27999296,"url":"https://github.com/chenyangkang/fasta2codeml","last_synced_at":"2026-04-07T05:31:53.604Z","repository":{"id":158723440,"uuid":"634154272","full_name":"chenyangkang/Fasta2Codeml","owner":"chenyangkang","description":"A codeml (PAML package) wrapper to make life easier. 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Dummy input unaligned multi-species fasta file (a single gene), and output codeml result.\n\n## Prerequisites\n1. Codeml (PAML version 4.10.6)\n2. MACSE (.jar form)\n3. MUSCLE\n4. RAXML\n\n5. biopython (v1.81, python package)\n6. newick (v1.9.0, python package)\n\nmust be installed beforehand\n\n# Installation\nSimply add ./script to your environment\n\n\n# Input data\n1. A single gene fasta sequence file (multi-species, not aligned).\n2. A text file which indicate the foreground species. One species each line.\n\n\n# Example\ncd to example/test_space/\n\n**Change the absolute path in the command lines below to to your path.**\n\n## For single fasta file mode\ntype:\n```\nFasta2Codeml.py \\\n--out_dir /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/test_space_single_gene \\\n--project_name Simple_test \\\n--foreground_file /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/foreground.txt \\\n--fasta /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/single_gene/CLOCK.fasta \\\n--muscle /beegfs/store4/chenyangkang/software/ParaAT2.0/muscle \\\n--macse /beegfs/store4/chenyangkang/software/macse_v2.07.jar \\\n--raxml /beegfs/store4/chenyangkang/software/standard-RAxML/raxml \\\n--codeml /beegfs/store4/chenyangkang/miniconda3/bin/codeml \\\n--boostrap 10 \\\n--codon_frac 0.5 \\\n--sp_frac 0.5\n\n```\n\n## For multi-file model (multi-cds file mode):\n```\nFasta2Codeml.py \\\n--out_dir /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/test_space_multi_cds \\\n--project_name Simple_multi_test \\\n--foreground_file /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/foreground.txt \\\n--multi_file \\\n--multi_file_list cds_list.txt \\\n--muscle /beegfs/store4/chenyangkang/software/ParaAT2.0/muscle \\\n--macse /beegfs/store4/chenyangkang/software/macse_v2.07.jar \\\n--raxml /beegfs/store4/chenyangkang/software/standard-RAxML/raxml \\\n--codeml /beegfs/store4/chenyangkang/miniconda3/bin/codeml \\\n--boostrap 10 \\\n--codon_frac 0.5 \\\n--sp_frac 0.5\n\n```\n\n# Workflow underneath\n1. Remove species that contain only \"N\"s.\n2. Run muscle alignment with 5 iterations.\n3. Refine alignment using MACSE.\n4. Replace frameshift(!) and stop codon with NNN using MACSE.\n5. Concatenate files (if in multi-file mode).\n6. Remove codon columns with more than 50% species missed, and remove species with more than 50% codons as \"NNN\" or \"---\".\n7. Build tree with raxml `-f a -x 42 -p 42 -m GTRGAMMA `.\n8. Co-filter fasta file and tree file. Trim and annotate tree with the foreground information provided. Output alignment as phylip format.\n9. Generate codeml configuration files for both branch-site null model (omega=1) and alternative model.\n10. Run both codeml model.\n11. Generate p values and other statistics using scipy.\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchenyangkang%2Ffasta2codeml","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchenyangkang%2Ffasta2codeml","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchenyangkang%2Ffasta2codeml/lists"}