Calculate phastCons

[laurafabre]

Hi,

I am currently using Progressive Cactus (via Docker) and would like to integrate Phast tools, particularly PhastCons, into my workflow. However, I am finding it challenging to determine the correct approach to run Phast tools with my existing setup, especially considering the various Cactus versions.
To make the context:
Input Alignment: I already have a HAL file generated from Progressive Cactus.
Goal: Generate a neutral model and calculate PhastCons scores using this alignment.

My questions are:

To generate the neutral model, should I convert the HAL file to MAF format first and then run Phast’s phyloFit binaries directly?. And for the cactus-hal2maf use the options: --noDupes --onlyOrthologs --noAncestors or are there any other specifications for generating the MAF to run Phast?
Alternatively, is there a way to compute PhastCons scores directly from the HAL file without converting it to MAF, leveraging the tools provided with Cactus or via a specific workflow?
Thanks in advance for your time!

[glennhickey]

Yes, because the halPhyloP tools are quite dated and not so well maintained, I recommend using cactus-hal2maf to make a MAF then following instructions from the Phast documentation from there.