Ancestral_karyotype_repertoire ------------------------------ Incorporate genes from collinearity blocks into the ancestral karyotype repertoire. .. rubric:: Parameters .. tabularcolumns:: column spec ========================= ======================================================================== 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. .. code-block:: python [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 .. rubric:: Quick start The original results are easily accessible at `wgdi-example `_