Orthologs.Phylogenetics.ETE3PAML

Integration of ETE3 for using PAML’s codeml.

Usage

Source

Orthologs.Phylogenetics.ETE3PAML(
    infile,
    species_tree,
    workdir,
    pamlsrc=None,
)

M1 model is best for orthology inferences.

Methods

Name Description
__init__() Initialize main variables/files to be used.
prune_tree() Prune branches for species not in the alignment file.
run() Run PAML using ETE.

__init__()

Initialize main variables/files to be used.

Usage

Source

__init__(infile, species_tree, workdir, pamlsrc=None)

Ensure that you have the correct path to your codeml binary. It should be in the paml /bin.

Parameters
infile: str

The input fasta file.

species_tree: str

The newick-formatted species tree.

workdir: str

The working directory for input and output.

pamlsrc: (str, optional) = None
The path to your codeml src if not in PATH, defaults to None

prune_tree()

Prune branches for species not in the alignment file.

Usage

Source

prune_tree(organisms_list, organisms_file=None, column_header="Organisms")

Keep branches in the species tree for species in the alignment file Some species may not be present in the alignment file due to lack of matching with blast or simply the gene not being in the genome.

Parameters
organisms_list: str

A list of species used to create the species tree.

organisms_file: (str, optional) = None

A file of the organisms in case in list is not provided, defaults to None

column_header: (str, optional) = "Organisms"
The name of the column in the file, defaults to “Organisms”

run()

Run PAML using ETE.

Usage

Source

run(outfile, tree="temptree.nw", model="M1")

The default model is M1 as it is best for orthology inference in our case. You can use models M2, M0, M3.

Parameters
outfile: str

The output PAML file.

tree: (str, optional) = "temptree.nw"

A newick-formatted species tree, defaults to “temptree.nw”

model: (str, optional) = "M1"
The PAML model to be run, defaults to “M1”