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ARB graphical DNA, RNA and amino acid sequence analysis tool

ARB is an application for genetic sequence analysis that includes tools for editing and aligning nucleotide and amino acid sequences. Features include routines for designing fluorescence in situ hybridization (FISH) probes and PCR and sequencing primers. Phylogenetic trees can be generated and sequences can be added to existing trees. ARB maintains links between the phylogenetic trees and sequences for database search and query. The Silva Comprehensive Ribosomal RNA Database (http://www.arb-silva.de/) maintains up-to-date databases. An active community of scientists exchanges tips on the ARB Yahoo! discussion group (http://tech.groups.yahoo.com/group/arb_users/). Citation: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371.

Version: 6.0.6 License: Restrictive/Distributable GitHub
Maintainers No Maintainer
Categories science
Homepage http://www.arb-home.de/
Platforms darwin
Variants -

"arb" depends on

lib (15)
build (3)

Ports that depend on "arb"

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Port notes

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Before running ARB you must set ARBHOME and add ARB to your PATH
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You have two options (A is easier, B is more difficult):

A) Easy - open a new terminal window and type arb_macsetup to set the necessary environment variables automatically. This script also enables keyboard shortcuts used in the sequence editor.

or

B) More difficult - follow the steps below:

1)
bash users add the following lines to your ~/.profile or to your ~/.bashrc

ARBHOME=${prefix}/share/arb;export ARBHOME
PATH=${prefix}/share/arb/bin:$PATH
export PATH

enter the following command:
. ~/.profile
2)
tcsh users add the following lines to your ~/.cshrc

setenv ARBHOME ${prefix}/share/arb
setenv PATH ${prefix}/share/arb:$PATH

enter the following command:
source ~/.cshrc

C) to set up ARB for another user on this computer log into their account and type ${prefix}/bin/arb_macsetup

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You can set up keyboard shortcuts manually by creating a text file in your home folder called .xmodmap that contains the text below:
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clear Mod1
clear Mod2
keycode 63 = Mode_switch
keycode 66 = Meta_L
keycode 69 = Meta_R
add Mod1 = Meta_L Meta_R
add Mod2 = Mode_switch

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Use keys Control+Command Arrow Key to jump over bases
Use Keys Option Arrow Key to pull in bases across alignment gaps
Use the right Command Key plus a letter key to activate a menu item
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Type 'arb' to start using ARB
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A demo data base is located at ${prefix}/share/arb/demo.arb

User generated macros, arb_tcp.dat and pt_servers have been preserved,
but you should keep backups of these just in case. They are located at:

${prefix}/share/arb/lib/macros/
${prefix}/share/arb/lib/arb_tcp.dat
${prefix}/share/arb/lib/pts/

Default settings are maintained at:

${prefix}/share/arb/lib/macros.default/
${prefix}/share/arb/lib/arb_tcp.dat.default

These notes can be viewed at any time by typing 'port notes arb'

Please cite: Wolfgang Ludwig, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Research. 32:1363-1371


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arb seems to have been updated (port version: 6.0.6, new version: 7.0.1)

livecheck ran: 1 day, 18 hours ago