An auxiliary script that migt help

[AhmedElsherbini]

Hi all,

Firstly, thank you for developing this nice tool.

Recently, I made this simple script that helps me to work with your binary file. My script aims to break down the binary matrix into the count of each species per the file, fetching the number of sequenced genome counts from NCBI assembly and dividing them to give a hint on the spread of the cluster of interest. Finally, draw a tree between those species based on the pre-defined NCBI taxonomy.

Firstly, if you have any feedback, I will be happy to get it. I hope I can benefit other colleagues with this script.

Secondly, for some hits, I get more than > 100 % (when I divide the hits per species over the number of this species genomes in the assembly database) meaning that I get hits more than sequenced genomes in the assembly database. I thought about fetching the number from the NCBI biosample database instead, I am reluctant though. What do you recommend?

Best regards,
Ahmed