---
name: "truncyk_check"
section: "1"
platform: "linux"
package: "infernal"
version: "1.0.2-2"
release: "Debian 7 (Wheezy)"
platforms: ["linux"]
url: "https://new.carta.tech/truncyk_check"
---

# truncyk\_check(1)

## NAME

- truncyk\_check - check alignment under the TrCYK model

  ## SYNOPSIS

**truncyk\_check** *\[options\]* *cmfile* *seqfile*

## DESCRIPTION

**trcyk** reads the covariance model (CM) in *cmfile* and aligns the sequences in  *seqfile* to that CM using the TrCYK model for incomplete data, using both the full-memory and divide-and-conquer approaches.  It checks that the scores from both methods match, that the alignments from both methods match, and that the score of each alignment matches the score returned by the program.

Because it does use the full-memory implementation of TrCYK it can be extremely memory intensive; checking only the scores with the  *--scoreonly* option or only the divide-and-conquer approach with the *--smallonly* option is advised for large models and/or long sequences.

## OPTIONS

- **-h**

  show help

- **--scoreonly**

  Check only the scores, not the alignments (saves memory).

- **--smallonly**

  Check only divide-and-conquer, not the full memory implementation (saves memory).

- **--stringent**

  Require the two parsetrees to be identical.