ancestral_karyotype

Generation of ancestral karyotypes from chromosomes that retain the same structure in modern species.

Parameters

Parameters	Standards and instructions
gff	Type: file | Default: - Cat the relevant ‘gff’ files into a file.
pep_file	Type: file | Default: none Cat the relevant ‘pep.fa’ files into a file.
ancestor	Type: file | Default: none This file requires you to provide.
mark	Type: str | Default: aak A shorthand for ancestral karyotype.
ancestor_gff	Type: file | Default: none Gff file of the created ancestral karyotype.
ancestor_lens	Type: file | Default: none Lens file of the created ancestral karyotype.
ancestor_pep	Type: file | Default: - Pep file of the created ancestral karyotype.
ancestor_file	Type: file | Default: - Updated the ancestral karyotype file.

Use command to enter the folder wgdi -ak ? >> total.conf Take out the parameter file.

[ancestral_karyotype]
gff = gff file (cat the relevant 'gff' files into a file)
pep_file = pep file (cat the relevant 'pep.fa' files into a file)
ancestor = ancestor file  (this file requires you to provide)
mark = aak
ancestor_gff =  result file
ancestor_lens =  result file
ancestor_pep =  result file
ancestor_file =  result file

Quick start

The original results are easily accessible at wgdi-example