Fighting with ARB

October 22nd, 2012 by eric

Trying to make ARB do ones bidding is often a challenge in patience and sanity, especially if one is not a daily user of this beast of a program.

1) Update arb_phyml to use PhyML version 20120412
After replacing the phyml binary, changes to the interactive menu in the new version of PhyML required changes to the script running it from ARB. Backup the original and copy this file into the arb/bin/ directory. Or use the interactive menu.

arb_phyml

2) Selecting many species at once
Use a regular expression in the SEARCH field, e.g. ‘/species1|species2|species3|species4/’

3) Regexp in Editing Fields
I had imported sequences of the form “16S ribosomal RNA [Marinobacter sp. ELB17, unfinished sequence: NZ_AAXY01000002] (-)strand” and I wanted new fields with just the stuff in the [brackets]. For some reason the asterisk ‘*’ was not working in the regexp field — it kept crashing ARB. So I used a plus ‘+’ instead et voila.

SEARCH --> MORE FUNCTIONS --> EDIT FIELDS OF SELECTED SPECIES
|readdb(full_name)|command(/16S.+\\[(.+)\\].+/\\1/)

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