---
name: "readseq"
section: "1"
platform: "linux"
package: "readseq"
version: "1-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/readseq"
---

# readseq(1)

Reads and writes nucleic/protein sequences in various formats

## NAME

readseq - Reads and writes nucleic/protein sequences in various formats

## SYNOPSIS

**readseq** *\[-options\] in.seq \> out.seq*

## DESCRIPTION

This manual page documents briefly the **readseq** command. This manual page was written for the Debian GNU/Linux distribution because the original program does not have a manual page. Instead, it has documentation in text form, see below.

**readseq** reads and writes biosequences (nucleic/protein) in various formats.  Data files may have multiple sequences. **readseq** is particularly useful as it automatically detects many sequence formats, and interconverts among them.

## FORMATS

- Formats which readseq currently understands:

  - \* IG/Stanford, used by Intelligenetics and others

  - \* GenBank/GB, genbank flatfile format

  - \* NBRF format

  - \* EMBL, EMBL flatfile format

  - \* GCG, single sequence format of GCG software

  - \* DNAStrider, for common Mac program

  - \* Fitch format, limited use

  - \* Pearson/Fasta, a common format used by Fasta programs and others

  - \* Zuker format, limited use. Input only.

  - \* Olsen, format printed by Olsen VMS sequence editor. Input only.

  - \* Phylip3.2, sequential format for Phylip programs

  - \* Phylip, interleaved format for Phylip programs (v3.3, v3.4)

  - \* Plain/Raw, sequence data only (no name, document, numbering)

  - \+ MSF multi sequence format used by GCG software

  - \+ PAUP's multiple sequence (NEXUS) format

  - \+ PIR/CODATA format used by PIR

  - \+ ASN.1 format used by NCBI

  - \+ Pretty print with various options for nice looking output. Output only.

  - \+ LinAll format, limited use (LinAll and ConStruct programs)

  - \+ Vienna format used by ViennaRNA programs

  - See the included "Formats" file for detail on file formats.

  ## OPTIONS

- **-help**

  Show summary of options.

- **-a\[ll\]**

  Select All sequences

- **-c\[aselower\]**

  Change to lower case

- **-C\[ASEUPPER\]**

  Change to UPPER CASE

- **-degap\[=-\]**

  Remove gap symbols

- **-i\[tem=2,3,4\]**

  Select Item number(s) from several

- **-l\[ist\]**

  List sequences only

- **-o\[utput=\]out.seq**

  Redirect Output

- **-p\[ipe\]**

  Pipe (command line, \<stdin, \>stdout)

- **-r\[everse\]**

  Change to Reverse-complement

- **-v\[erbose\]**

  Verbose progress

- **-f\[ormat=\]# Format number for output, or**

      \-f\[ormat=\]Name Format name for output:\
       1\. IG/Stanford           11. Phylip3.2       \
       2\. GenBank/GB            12. Phylip          \
       3\. NBRF                  13. Plain/Raw       \
       4\. EMBL                  14. PIR/CODATA      \
       5\. GCG                   15. MSF             \
       6\. DNAStrider            16. ASN.1           \
       7\. Fitch                 17. PAUP/NEXUS      \
       8\. Pearson/Fasta         18. Pretty (out-only)\
       9\. Zuker (in-only)       19. LinAll          \
      10\. Olsen (in-only)       20. Vienna

  Pretty format options:

- **-wid\[th\]=#**

  Sequence line width

- **-tab=#**

  Left indent

- **-col\[space\]=#**

  Column space within sequence line on output

- **-gap\[count\]**

  Count gap chars in sequence numbers

- **-nameleft, -nameright\[=#\]**

  Name on left/right side \[=max width\]

- **-nametop**

  Name at top/bottom

- **-numleft, -numright**

  Seq index on left/right side

- **-numtop, -numbot**

  Index on top/bottom

- **-match\[=.\]**

  Use match base for 2..n species

- **-inter\[line=#\]**

  Blank line(s) between sequence blocks

## EXAMPLES

- readseq

        \-- for interactive use

- readseq my.1st.seq my.2nd.seq -all -format=genbank -output=my.gb

        \-- convert all of two input files to one genbank format output file

- readseq my.seq -all -form=pretty -nameleft=3 -numleft -numright -numtop -match

        \-- output to standard output a file in a pretty format

- readseq my.seq -item=9,8,3,2 -degap -CASE -rev -f=msf -out=my.rev

        \-- select 4 items from input, degap, reverse, and uppercase them

- cat \*.seq \| readseq -pipe -all -format=asn \> bunch-of.asn

        \-- pipe a bunch of data thru readseq, converting all to asn

## SEE ALSO

The programs are documented fully in text form. See the files in */usr/share/doc/readseq*

## AUTHOR

This manual page was written by Stephane Bortzmeyer \<bortzmeyer@debian.org\>, for the Debian GNU/Linux system (but may be used by others).