---
name: "weight"
section: "1"
platform: "linux"
package: "biosquid"
version: "1.9g+cvs20050121-15.1+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/weight"
---

# weight(1)

calculates sequence weights for an alignment

## NAME

weight - calculates sequence weights for an alignment

## SYNOPSIS

**weight** \[-options\] \<alignment file\>

## DESCRIPTION

This manual page documents briefly the **weight** command.

**weight** is a program that calculates weights for a sequence alignment.

## OPTIONS

Available options:

- **-b \<f\>**

  Use BLOSUM weighting scheme at \<f\> fractional identity.

- **-f \<f\>**

  Filter out seqs w/ fractional ident \> \<x\> \[0-1\].

- **-h**

  Help; print version and usage info.

- **-o \<file\>**

  Save weight-annotated alignment in \<outfile\>.

- **-p**

  Use position based weight scheme (Henikoff & Henikoff).

- **-s \<n\>**

  Sample \<n\> sequences at random into a new alignment.

- **-v**

  Use Voronoi weight scheme (Sibbald & Argos).

- **--informat \<s\>**

  Specify alignment file format \<s\>.\
   Allowed formats: SELEX, MSF, Clustal, a2m, PHYLIP.

- **--quiet**

  Suppress verbose banner.

## SEE ALSO

[**afetch**(1)](/afetch/1.md), [**alistat**(1)](/alistat/1.md), [**compalign**(1)](/compalign/1.md), [**compstruct**(1)](/compstruct/1.md), [**revcomp**(1)](/revcomp/1.md), [**seqsplit**(1)](/seqsplit/1.md), [**seqstat**(1)](/seqstat/1.md), [**sfetch**(1)](/sfetch/1.md), [**shuffle**(1)](/shuffle/1.md), [**sindex**(1)](/sindex/1.md), [**sreformat**(1)](/sreformat/1.md), [**stranslate**(1)](/stranslate/1.md),\

## AUTHOR

```
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX  : 1-314-362-2157
Email: eddy@genetics.wustl.edu
```

This manual page was written by Nelson A. de Oliveira \<naoliv@gmail.com\>, for the Debian project (but may be used by others).