---
name: "timescorealn"
section: "1"
platform: "linux"
package: "kalign"
version: "1:3.3-1+b3"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/timescorealn"
---

# timescorealn(1)

Global and progressive multiple sequence alignment

## NAME

timescorealn - Global and progressive multiple sequence alignment

## SYNOPSIS

**timescorealn-avx2** \[*-options*\]   *-test \<test sequences\> -ref \<reference alignment\> -program \<kalign\|clustalo\|muscle\> -o \<outfile\>*

## DESCRIPTION

\[2020-08-04 21:41:11\] :   ERROR : No test file

-

  (time\_and\_score\_aln.c line 111)

NOTE: the program appends results to the output file.

## OPTIONS

- **--scratch**

  : Scratch directory. \[NA\]

Usage: timescorealn-avx2 \[-options\]   **-test** \<test sequences\> **-ref** \<reference alignment\> **-program** \<kalign\|clustalo\|muscle\> **-o** \<outfile\>

NOTE: the program appends results to the output file.

- **--scratch**

  : Scratch directory. \[NA\]

\[2020-08-04 21:41:11\] : WARNING : Something went wrong. Use this program like this:

-

  (time\_and\_score\_aln.c line 154)

Usage: timescorealn-avx2 \[-options\]   **-test** \<test sequences\> **-ref** \<reference alignment\> **-program** \<kalign\|clustalo\|muscle\> **-o** \<outfile\>

NOTE: the program appends results to the output file.

- **--scratch**

  : Scratch directory. \[NA\]

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.