search

eead-csic-compbio / allopolyploids

PhyloSD: Phylogenomic Subgenome Detection pipeline
GNU General Public License v3.0
7 stars 1 forks source link

Application data #1

Open yuanw-18 opened 2 years ago

yuanw-18 commented 2 years ago

Hi,

It’s really exciting that you can develop such software.

I have an allotetraploid and its relative diploid. I only have their genome data(scaffold level) without transcriptome data. Can my data be used to distinguish subgenome with this software？

Thank you!

rubenzaragoza commented 2 years ago

Good morning WangYuan20190517,

Thank you very much for your interest in our software.

PhyloSD works well with genomic and transcriptomic sequences, either full or partial sequences, but you need to have those genes annotated. The more starting sequences and phylogenetic information on the diploid species you have, the more robust the results for the allopolyploid species of the genus to study will be. All the best

yuanw-18 commented 2 years ago

Thank you for your enthusiastic reply. I will try soon.

eead-csic-compbio commented 2 years ago

Hi @WangYuan20190517 , if you do try it out we'll appreciate feedback on the tutorial and how to improve it, thanks!