CodonU.phylogenetic_analysis

Submodules

Package Contents

Functions

phy_clustal_w(bin_path, handle[, res_folder_path])

Makes the multiple sequence alignment with ClustalW. For details visit http://www.clustal.org/clustal2

phy_clustal_o(bin_path, handle[, res_folder_path])

Makes the multiple sequence alignment with ClustalO. For details visit http://www.clustal.org/omega

generate_phylo_input(file_lst[, file_name, folder_path])

Generates the alignment input file
CodonU.phylogenetic_analysis.phy_clustal_w(bin_path: str, handle: str, res_folder_path: str = 'Report')

Makes the multiple sequence alignment with ClustalW. For details visit http://www.clustal.org/clustal2

Parameters:

  • bin_path – Path to the binary file of ClustalW

  • handle – Handle to the file, or the filename as a string

  • res_folder_path – The path of folder where the file will be saved

CodonU.phylogenetic_analysis.phy_clustal_o(bin_path: str, handle: str, res_folder_path: str = 'Report')

Makes the multiple sequence alignment with ClustalO. For details visit http://www.clustal.org/omega

Parameters:

  • bin_path – Path to the binary file of ClustalO

  • handle – Handle to the file, or the filename as a string

  • res_folder_path – The path of folder where the file will be saved

CodonU.phylogenetic_analysis.generate_phylo_input(file_lst: list[str], file_name: str = 'phylo_input', folder_path: str = 'Report')

Generates the alignment input file

Parameters:

  • file_lst – List containing paths of fasta file

  • file_name – Output filename

  • folder_path – Folder name