pangenomes_from_files_mmseqs: Individual pangenome clustering from file-list

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

Individual pangenome clustering from file-list

Description

This is an internal function for the workflow of pangenomes

Usage

pangenomes_from_files_mmseqs(
  file_list,
  i,
  coverage,
  identity,
  evalue,
  n_cores,
  cov_mode,
  cluster_mode,
  folder
)

Arguments

file_list	a list of file_list (genomes of the pangenome)
i	The pangenome number
coverage	min coverage for homologous cluster
identity	min identitity for homologous cluster
evalue	max E-value for homologous cluster
n_cores	number of cores to use
cov_mode	coverage mode
cluster_mode	cluster mode
folder

Value

A list with two tables, the membership of the pangenome, and the gene/protein frequency.

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.