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

# pbsDecode(1)

Decode a binary encoding of a probabilistic biological sequence

## NAME

pbsDecode - Decode a binary encoding of a probabilistic biological sequence

## DESCRIPTION

Decode a binary encoding of a probabilistic biological sequence (PBS).  Outputs a table with a row for each position in the sequence and a column for each base, such that the (i,j)th value is the probability of base j at position i.  The same codefile that was used to encode the sequence should be given.

-

  This program performs the inverse function of pbsEncode.

## EXAMPLE

Decode an encoded ancestral sequence:

-

  pbsDecode anc.human-mouse.bin mammal.code \> anc.human-mouse.probs

where "anc.human-mouse.bin" is a binary encoding of an ancestral sequence produced by pbsEncode or prequel, and "mammal.code" is a codefile produced by pbsTrain.

## OPTIONS

**--start**, **-s** \<sidx\>

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  Decode only the subsequence starting at position \<sidx\>. Indexing starts with 1.

**--end**, **-e** \<eidx\>

-

  Decode only the subsequence ending at position \<eidx\>. Indexing starts with 1.

**--discard-gaps**, **-G** Do not report gaps in the PBS.

**--help**, **-h**

-

  Produce this help message.