Alignment Dependencies Installation

To change the alignment method, modify the alignment_method parameter in the params.yaml file.

To use the MUSCLE, CLUSTALW, and MAFFT alignment methods, please ensure the following dependencies are installed. 1. MUSCLE:

• Download the appropriate version from the MUSCLE 5.1.0 release: - MUSCLE 5.1.0 Release

• Windows:

  • Download muscle5.1.win64.exe

• Linux:

  • Download muscle5.1.linux_intel64

• Place the downloaded file in the aphylogeo/bin directory.

2. CLUSTALW: - Download the latest version from the official website:

   • CLUSTALW Download

   • Follow the installation instructions.

   • Ensure the CLUSTALW executable is in the aphylogeo/bin directory.

3. MAFFT: - Download the latest version from the official website:

   • MAFFT Download

   • Follow the installation instructions.

   • Windows:

     • Place the mafft-win folder in the aphylogeo/bin directory.

   • Linux:

     • Create a folder named mafft-linux64 in the aphylogeo/bin directory.

     • Move the mafft.bat file into the mafft-linux64 folder.

Ensure that all executables are accessible in the specified directories before running the alignment methods.