---
name: "zalign"
section: "1"
platform: "linux"
package: "zalign"
version: "0.9.1-5"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/zalign"
---

# zalign(1)

parallel local alignment of biological sequences

## NAME

zalign - parallel local alignment of biological sequences

## SYNOPSIS

**zalign** \[-s scores\] \[-S split\] \[-H hblk\] \[-V vblk\] file1 file2

## DESCRIPTION

zAlign is a local sequence aligner, especially intended for use with large biological DNA sequences, with more than 1Mbp (Millions of base pairs). It uses the Smith-Waterman exact algorithm with affine gap cost function to perform this task.

### General options:

- **-h**

  display this help and exit

- **-s** \<scores\>

  specify a comma-separated list of scores to be used while calculating aligment matrices throughout the program. The list must be in the format "-sMATCH,MISMATCH,GAP\_OPEN,GAP\_EXTENSION" (without quotes), and is parsed in this PRECISE order; no spaces are allowed between values. If there are any unspecified parameters, these are set to default values and a warning message is issued; exceeding parameters are discarded

### Stage 2 options:

- **-S** \<split\>

  (mpialign only) number of parts in which to split the alignment matrix; after this step a cyclic block model is applied, subdividing each part equally between all available nodes

- **-H** \<hblk\>

  (mpialign only) number of horizontal subdivisions made by each node to its alignment submatrix; since this value defines block width, a good choice should allow two full matrix lines to fit the processor's cache pages, improving algorithm performance

- **-V** \<vblk\>

  (mpialign only) number of vertical subdivisions made by each node to its alignment submatrix; this value directly affects the amount of internode communication and is used ONLY if 'split' is set to 1, otherwise it is set to the number of available nodes