---
name: "pbsEncode"
section: "1"
platform: "linux"
package: "phast"
version: "1.7+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pbsEncode"
---

# pbsEncode(1)

Produce an approximate binary encoding of a probabilistic

## NAME

pbsEncode - Produce an approximate binary encoding of a probabilistic

## DESCRIPTION

Produce an approximate binary encoding of a probabilistic biological sequence (PBS), as defined by a text file ("input.probs") with a row for each position in the sequence and a column for each base.  The (i,j)th value in this table should be the probability of base j at position i.  Columns should be white-space delimited.  The encoding will be as defined by "codefile", which should be in the format used by pbsTrain.

This program performs the inverse function of pbsDecode.

## EXAMPLE

Encode the probabilities in a file "anc.human-mouse.probs", produced by prequel, using a code file "mammals.code", produced by pbsTrain. pbsEncode anc.human-mouse.probs mammals.code \> anc.human-mouse.bin

## OPTIONS

**--discard-gaps**, **-G**

- Discard gaps in the PBS.

  Gaps in the input data are assumed

-

  to be represented by rows consisting of a single "-" character.

**--help**, **-h** Produce this help message.