https://github.com/chenyangkang/fasta2codeml
A codeml (PAML package) wrapper to make life easier. Dummy input unaligned multi-species fasta file (a single gene), and output codeml result.
https://github.com/chenyangkang/fasta2codeml
codeml ecology molecular-evolution natural-selection paml selection
Last synced: about 1 month ago
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A codeml (PAML package) wrapper to make life easier. Dummy input unaligned multi-species fasta file (a single gene), and output codeml result.
- Host: GitHub
- URL: https://github.com/chenyangkang/fasta2codeml
- Owner: chenyangkang
- License: mit
- Created: 2023-04-29T08:06:40.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2024-12-12T20:25:50.000Z (6 months ago)
- Last Synced: 2025-05-08T22:57:34.865Z (about 1 month ago)
- Topics: codeml, ecology, molecular-evolution, natural-selection, paml, selection
- Language: Python
- Homepage:
- Size: 1.45 MB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Fasta2Codeml
A codeml (PAML package) wrapper to make life easier. Dummy input unaligned multi-species fasta file (a single gene), and output codeml result.
## Prerequisites
1. Codeml (PAML version 4.10.6)
2. MACSE (.jar form)
3. MUSCLE
4. RAXML
5. biopython (v1.81, python package)
6. newick (v1.9.0, python package)
must be installed beforehand
# Installation
Simply add ./script to your environment
# Input data
1. A single gene fasta sequence file (multi-species, not aligned).
2. A text file which indicate the foreground species. One species each line.
# Example
cd to example/test_space/
**Change the absolute path in the command lines below to to your path.**
## For single fasta file mode
type:
```
Fasta2Codeml.py \
--out_dir /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/test_space_single_gene \
--project_name Simple_test \
--foreground_file /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/foreground.txt \
--fasta /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/single_gene/CLOCK.fasta \
--muscle /beegfs/store4/chenyangkang/software/ParaAT2.0/muscle \
--macse /beegfs/store4/chenyangkang/software/macse_v2.07.jar \
--raxml /beegfs/store4/chenyangkang/software/standard-RAxML/raxml \
--codeml /beegfs/store4/chenyangkang/miniconda3/bin/codeml \
--boostrap 10 \
--codon_frac 0.5 \
--sp_frac 0.5
```
## For multi-file model (multi-cds file mode):
```
Fasta2Codeml.py \
--out_dir /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/test_space_multi_cds \
--project_name Simple_multi_test \
--foreground_file /beegfs/store4/chenyangkang/DEV/Fasta2Codeml/example/foreground.txt \
--multi_file \
--multi_file_list cds_list.txt \
--muscle /beegfs/store4/chenyangkang/software/ParaAT2.0/muscle \
--macse /beegfs/store4/chenyangkang/software/macse_v2.07.jar \
--raxml /beegfs/store4/chenyangkang/software/standard-RAxML/raxml \
--codeml /beegfs/store4/chenyangkang/miniconda3/bin/codeml \
--boostrap 10 \
--codon_frac 0.5 \
--sp_frac 0.5
```
# Workflow underneath
1. Remove species that contain only "N"s.
2. Run muscle alignment with 5 iterations.
3. Refine alignment using MACSE.
4. Replace frameshift(!) and stop codon with NNN using MACSE.
5. Concatenate files (if in multi-file mode).
6. Remove codon columns with more than 50% species missed, and remove species with more than 50% codons as "NNN" or "---".
7. Build tree with raxml `-f a -x 42 -p 42 -m GTRGAMMA `.
8. Co-filter fasta file and tree file. Trim and annotate tree with the foreground information provided. Output alignment as phylip format.
9. Generate codeml configuration files for both branch-site null model (omega=1) and alternative model.
10. Run both codeml model.
11. Generate p values and other statistics using scipy.