I'm trying to write a script which would use hmmpgmd to predict homology to query protein sequence. There is an example on how to do this mentioned in documentation for hmmpgmd (https://github.com/Janelia-Farm-Xfam/Bio-HMM-Logo/blob/master/src/src/hmmpgmd_client_example.pl). However this example doesn't have clear comments and returned data fields are not properly described (almost always limeted to just a cryptic name).

So I'm writing here so that maybe there is a person who has experience using hmmpgmd, and more particularly experience reading matched alignment positions from hmmpgmd binary output.