ancestral_karyotype.rst

ancestral_karyotype

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

Parameters

column spec

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