I am using Progressive Cactus to align mosquito genomes. Mosquito genomes are highly heterozygous with levels of divergence of >1% between chromosomes in the same individual. Most of my runs with ProgCactus seem comparable to TBA, but I was curious as to whether a tuning of the config file may allow for longer alignments in some regions. The issues section on your github site mentions the python script blastParametersScript.py, but I was still unclear on how this relates to the config file settings.
Thank you for your time and support of a great program!
Dear Dr. Hickey,
I am using Progressive Cactus to align mosquito genomes. Mosquito genomes are highly heterozygous with levels of divergence of >1% between chromosomes in the same individual. Most of my runs with ProgCactus seem comparable to TBA, but I was curious as to whether a tuning of the config file may allow for longer alignments in some regions. The issues section on your github site mentions the python script blastParametersScript.py, but I was still unclear on how this relates to the config file settings.
Thank you for your time and support of a great program!