SelectionPressureAnalysis

This repository provides custom scripts (i.e., pseudopipeline) to analyze selection pressure across multiple genes simultaneously.

Pipeline Overview

The pipeline includes the following steps:

1. Retrieve CDS Sequences of Orthologous Genes
   Extract CDS (coding sequence) data for a set of orthologous genes.

2. Combine the Fasta Sequences
   Merge the individual fasta files of sequences into a single file.

3. Clean and Remove Duplicates
   Clean the sequences and ensure only unique sequences are present in each fasta file.

4. Align Sequences Using MAFFT
   Perform sequence alignment using the MAFFT algorithm.

5. Convert Fasta to PHYLIP Format
   Convert the aligned sequences from Fasta to PHYLIP format (version 3.2).

6. Apply pal2nal
   Use pal2nal to synchronize the coding sequences with the protein sequences.

7. Generate Phylogenetic Trees Using RAxML
   Build phylogenetic trees based on the aligned sequences using RAxML.

8. Perform CODEML Analysis
   Conduct CODEML analysis to estimate selection pressures on the gene sequences.

Requirements

To run these scripts, you will need to install the necessary tools and packages, including:

• MAFFT
• pal2nal
• RAxML
• CODEML (from PAML)

Please ensure all required dependencies are installed before running the pipeline.