ancestral_karyotype_repertoire

Incorporate genes from collinearity blocks into the ancestral karyotype repertoire.

Parameters

Parameters	Standards and instructions
blockinfo	Type: file | Default: - Output result of parameter -bi and -c.
blockinfo_reverse	Type: bool | Default: false The two species aligned swap positions.
gff1	Type: file | Default: - Cat the relevant ‘gff’ files into a file.
gff2	Type: file | Default: - Cat the relevant ‘gff’ files into a file.
gap	type: int | Default: 5 Minimum number of genes bounded by collinear genes corresponds to two ordered protogenes.
ancestor	Type: file | Default: none This file requires you to provide.
ancestor_new	Type: file | Default: none Updated the ancestor file of ancestral karyotype..
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_pep_new	Type: file | Default: - Updated the pep file of ancestral karyotype.

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

[ancestral_karyotype_repertoire]
blockinfo =  block information (*.csv)
# blockinfo: processed *.csv
blockinfo_reverse = False
gff1 =  gff1 file (*.gff)
gff2 =  gff2 file (*.gff)
gap = 5
mark = aak1s
ancestor = ancestor file
ancestor_new =  result file
ancestor_pep =  ancestor pep file
ancestor_pep_new =  result file
ancestor_gff =  result file
ancestor_lens =  result file

Quick start

The original results are easily accessible at wgdi-example