---
name: "blixemh"
section: "1"
platform: "linux"
package: "blixem"
version: "4.44.1+dfsg-7.1+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/blixemh"
---

# blixemh(1)

display multiple alignments against a reference sequence

## NAME

blixemh - display multiple alignments against a reference sequence

## DESCRIPTION

-

  Blixem - display multiple alignments against a reference sequence.

-

  Usage: blixem \[options\] \[\<sequence\_file\>\] \<data\_file\> \[X options\]

-

  \<sequence\_file\> contains the reference sequence in FASTA format. \<data\_file\> is a GFF v3 file containing alignments and other features. If \<sequence\_file\> is omitted, \<data\_file\> should contain the reference sequence in FASTA format, below a comment line that reads ##FASTA.

-

  Both \<sequence\_file\> and \<data\_file\> can be substituted by "-" for reading from stdin (pipe).  If \<sequence\_file\> is piped, the first line should contain the sequence name and the second the sequence itself.

-

  Options:

- **-t** \<type\>, **--display-type=**\<type\>

  MANDATORY

-

  Whether to display sequences in nucleotide or protein mode. Must be one of:

-

  N = nucleotide P = protein

**-a** \<names\>, **--alignment-names=**\<names\>

-

  Specify a string giving the names of the alignments, e.g. "EST\_mouse EST\_human" etc.

**-c** \<file\>, **--config-file=**\<file\>

-

  Read configuration options from 'file'.

**--abbrev-title-on**

-

  Abbreviate window title prefixes

**--abbrev-title-off**

-

  Do not abbreviate window title prefixes

**--compiled**

-

  Show package compile date.

**-d** \<data\_file\>, **--data-file=**\<data\_file\>

-

  Alternative way of specifying \<data\_file\> using an argument

**--dataset**

-

  Optional string to indicate a data-set that the alignments are from.

**-e** \<sequence\_file\>, **--sequence-file=**\<sequence\_file\>

-

  Alternative way of specifying \<sequence\_file\> using an argument

**--dotter-first-match**

-

  Call Dotter on the first match to the right of the default start coord.

**--fetch-server** \<nodeid:port\>

-

  Causes Blixem to get sequences from a fetch server at machine 'nodeid' on the given port (default 22100).

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

-

  More detailed usage information.

**--hide-big-picture**

-

  Hide the big picture section on start-up.

**--hide-inactive-strand**

-

  Hide the inactive strand (i.e. the reverse strand, or the forward strand if the **-R** option is used).

**--highlight-diffs**

-

  Enable 'highlight differences' mode, where mismatches (rather than matches) are highlighted.

**--invert-sort**

-

  Invert sorting order

**-m** \<from\[:to\]\>, **--map-coords=**\<from\[:to\]\>

-

  Map the coordinate system so that the given 'from' coordinate maps to the given 'to' coordinate (or to '1' if 'to' is not given).

**-n**, **--negate-coords**

-

  When showing the reverse strand, negate the display coordinates.

**-o** \<n\>, **--offset=**\<n\>

-

  Offset the reference sequence coordinate system by n.

**--optional-data**

-

  Parse additional data such as organism and tissue-type on start-up.

**--remove-input-files**

-

  Delete the input files after they have been parsed.

**-r**, **--reverse-strand**

-

  Indicates that the given reference sequence is the reverse strand.

**--save-temp-files**

-

  Save any temporary files created by Blixem.

**--show-coverage**

-

  Display the coverage section on start-up.

**--sort-mode=**\<mode\>

-

  Default sort mode. Use **--help** option to see details.

**--squash-matches**

-

  Compress the alignment lists on start-up.

**-s** \<n\>, **--start-coord=**\<n\>

-

  Start with the display centred on coordinate n.

**--start-next-match**

-

  Start with the display centred on the first match to the right of the default start coord.

**-y** \<file\>, **--styles-file=**\<file\>

-

  Read color options from a key-value file. Use **--help** option to see details.

**--version**

-

  Show package version number.

**-z** \<start:end\>, **--zoom-range=**\<start:end\>

-

  Specify the initial range of coordinates to zoom the big picture in to.

**--zoom-whole**

-

  Start with the big picture zoomed out to view the full reference sequence range.

-

  Some X options: **-acefont** \<font\> Main font. **-font**    \<font\> Menu font.

**-----**

-

  Written by Gemma Barson \<gb10@sanger.ac.uk\> Based on original code by Erik Sonnhammer \<Erik.Sonnhammer@sbc.su.se\>

-

  Reference: Sonnhammer ELL & Durbin R (1994). A workbench for Large Scale

-

  Sequence Homology Analysis. Comput. Applic. Biosci. 10:301-307.

-

  See http://www.sanger.ac.uk/resources/software/seqtools/ for more info.

-

  Copyright (c) 2009-2015: Genome Research Ltd. Blixem is distributed under the GNU General Public License; see http://www.gnu.org/copyleft/gpl.txt

- Version 4.44.1

  14:27:56 Oct 19 2017

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.