Ancestral_karyotype ------------------- Generation of ancestral karyotypes from chromosomes that retain the same structure in modern species. .. rubric:: Parameters .. tabularcolumns:: column spec ========================= ======================================================================== 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. .. code-block:: python [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 .. rubric:: Quick start The original results are easily accessible at `wgdi-example `_