Section 8-7: Hints on additional software

[ Previous chapter ][ This chapter ][ Next chapter ] Many additional single sequence analysis programs are available as public domain programs. Others come as shareware , which means that you are free to try it out but should register (and pay a fee) if you use the programs regularly. This BioCompanion is shareware, too. Keep in mind that you verified the license status of a software program before installation or before using it. Software piracy is illegal and punishable by law.

The avialability of these programs might vary. Some authors distribute the software via floppy disks or internet, some use electronic mail.

SECURITY ADVICE: Be sure that you are aware of ramifications if you request or install programs which are possibly of dubious origin. Viruses, trojan horses or other security-related issues will render any activities as PROHIBITED unless the installation has been allowed by the system manager and/or the person responsible for software maintenance at your site. IN COMMERCIAL ENVIRONMENTS, YOU ARE USUALLY NOT ALLOWED TO INSTALL SOFTWARE YOURSELF.

SECURITY ADVICE: Programs which are obtained from sources which do not commit or offer to maintain the software are dangerous if large projects require error-free operation. Make sure that you are capable to fix problems yourself before proceeding. Likewise, make sure that the output can be VALIDATED with known examples - the fact that a program does not crash is not proofing its output quality.

Subsection 8.7.1

Benefits of additional software

available on personal computers and Macintoshes.
programs usually feature a very convenient user interface
rarely used or very sophisticated algorithms become available
close to 'up-to-date' science
uncovered areas (such as phylogeny) can be efficiently targeted

Subsection 8.7.2

Disadvantages

Usually, little installation or scientific support is provided in academic environments and public domain software.

You might observe 'less refined features', commonly referred to as 'bugs', which might be not as obvious as a program or computer crash. You need to validate proper operation with known examples before proceeding.
Depending on your computer (workstation, PC, etc.) you will face a potentially significant danger for your environment: viruses and other malicious effects might cause very undesired desasters (see above); this applies specifically to binary-only distributions.
You will typically need to reformat your data in order to use the additional software if you employ the GCG environment as default.

Subsection 8.7.3

Data transfer and formatting

In order to utilise the additional software, you will possibly need to transfer your sequence data to STADEN format, i.e., you will strip all non-sequence information from the sequence and transfer the data to the local computer with 'ftp' or a similar file transfer protocol. This is in particular useful if you use the WWW interface to access programs which will execute jobs remotely. Find out what the format of the sequence is, edit it manually (if required) and try one of the programs of the GCG package. To get information about GCG's reformatting programs , use

% genmanual sequence_exchange

[next page] , or [overview] , or [table of contents]