HMMER3 is stubborn

We've had a couple of reports of some less-than-intuitive behavior of HMMER3 on poor-scoring sequences. As one correspondent described it, HMMER3 is stubborn. It will refuse to score and align certain low-scoring sequences no matter what options you try to set. It's probably worth explaining this behavior in public, partly because it's an opportunity for … Continue reading HMMER3 is stubborn

Extracting HMMER results to sequence files: Easel miniapplications

The HMMER and Infernal code includes some hidden tools: the Easel library, and its "miniapplications". Easel is our code library (in the easel subdirectory of both HMMER and Infernal), and the miniapplications (in easel/miniapps) are a set of command line utilities that we use for manipulating sequence data. For example, esl-reformat is a utility for … Continue reading Extracting HMMER results to sequence files: Easel miniapplications