---
name: "pynast"
section: "1"
platform: "linux"
package: "pynast"
version: "1.2.2-4"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/pynast"
---

# pynast(1)

alignment of short DNA sequences

## NAME

PyNAST - alignment of short DNA sequences

## SYNOPSIS

**pynast** \[*options*\] *{-i input\_fp -t template\_fp}*

## DESCRIPTION

\[\] indicates optional input (order unimportant) {} indicates required input (order unimportant)

### Example usage:

-

  pynast **-i** my\_input.fasta **-t** my\_template.fasta

## OPTIONS

- **--version**

  show program's version number and exit

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

  show this help message and exit

- **-t** TEMPLATE\_FP, **--template\_fp**=*TEMPLATE\_FP*

  path to template alignment file \[REQUIRED\]

- **-i** INPUT\_FP, **--input\_fp**=*INPUT\_FP*

  path to input fasta file \[REQUIRED\]

- **-v**, **--verbose**

  Print status and other information during execution \[default: False\]

- **-p** MIN\_PCT\_ID, **--min\_pct\_id**=*MIN\_PCT\_ID*

  minimum percent sequence  identity to consider a sequence a match \[default: 75.0\]

- **-l** MIN\_LEN, **--min\_len**=*MIN\_LEN*

  minimum sequence length to include in NAST alignment \[default: 1000\]

- **-m** PAIRWISE\_ALIGNMENT\_METHOD, **--pairwise\_alignment\_method**=*PAIRWISE\_ALIGNMENT\_METHOD*

  method for performing pairwise alignment \[default: uclust\]

- **-a** FASTA\_OUT\_FP, **--fasta\_out\_fp**=*FASTA\_OUT\_FP*

  path to store resulting alignment file \[default: derived from input filepath\]

- **-g** LOG\_FP, **--log\_fp**=*LOG\_FP*

  path to store log file \[default: derived from input filepath\]

- **-f** FAILURE\_FP, **--failure\_fp**=*FAILURE\_FP*

  path to store file of seqs which fail to align \[default: derived from input filepath\]

- **-e** MAX\_E\_VALUE, **--max\_e\_value**=*MAX\_E\_VALUE*

  Depreciated. Will be removed in PyNAST 1.2

- **-d** BLAST\_DB, **--blast\_db**=*BLAST\_DB*

  Depreciated. Will be removed in PyNAST 1.2

## SEE ALSO

http://pynast.sourceforge.net