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

# trcyk(1)

## NAME

- trcyk - align sequences to a CM under the TrCYK model

  ## SYNOPSIS

**trcyk** *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.

The output gives the name of each aligned sequence, the score for the alignment, and the alignment itself. The '~' character in the sequence indicates residues that have been treated as missing data.