Free to run software for linux

VBox Runner 0.2 provides you with a small but very useful KRunner module which can allow you to run your VirtualBox virtual machines from KRunner. This product will be an excellent choice for everyone.

Sudo (su "do") allows a system administrator to give certain users (or groups of users) the ability to run some (or all) commands as root or another user while logging the commands and arguments.
The Sudo project is free software and is distributed under an ISC-style license.
Enhancements:
- This release adds support for IPv6.
- It has a fix for the installation path of the sudo_noexec shared object and a change to support compilation on old-style K&R compilers.

Netpet-CMS project provides easy-going deployment and administration of Web sites, newsletters, and banners. After a short introduction, even users with little experience are capable using Netpet-CMS.

Furthermore, you dont need any specially configured server to run Netpet CMS, so you can install Netpet CMS on standard cheap Web hosting accounts.

DOMjudge is an automated judge system to run programming contests.
Main features:
- Lightweight, depends on standard software to do its task
- Webinterface for portability and simplicity
- Scalable: distributed judging is easy
- Modular system for plugging in languages/compilers
- Features rejudging, clarifications, detailed submission/judging info
- Designed with security in mind
- Has been used in live contests
- Its Open Source, Free Software

SimDock project is a fast and fully configurable dock bar for Linux. It is written in C++ and wxWidgets, and does not require 3D acceleration to run.

Test-Run is an improved test harness for scripts that emit TAP (Test Anything Protocol). It was forked from Test::Harness, and it uses TAP::Parser.

The project is used to analyze the output of the scripts and present it to the user in a summarized form. Test-Run features separation of the test-running backend and the command line frontend, a "runprove" utility for running tests from the command line, a plugin-system, and colors for the summary line.

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search.

Parameters:

fasta (Excl)
Fasta program

query (Sequence)
Query sequence File
pipe: seqfile

seqtype (Excl)
Is it a DNA or protein sequence (-n)

protein_db (Excl)
Protein Database

nucleotid_db (Excl)
Nucleotid Database

break_long (Integer)
Break long library sequences into blocks (-N)

ktup (Integer)
ktup : sensitivity and speed of the search (protein:2, DNA:6)

optcut (Integer)
OPTCUT : the threshold for optimization. (-c)

gapinit (Integer)
Penalty for gap initiation (-12 by default for fasta with proteins, -16 for DNA) (-f)

gapext (Integer)
Penalty for gap extention (-2 by default for fasta with proteins, -4 for DNA) (-g)

high_expect (Float)
Maximal expectation value threshold for displaying scores and alignments (-E)

low_expect (Float)
Minimal expectation value threshold for displaying scores and alignments (-F)

nucleotid_match (Integer)
Reward for a nucleotid match (-r)

nucleotid_mismatch (Integer)
Penalty for a nucleotid mismatch (-r)

matrix (Excl)
Scoring matrix file (-s)

X_penalty (Integer)
Penalty for a match to X (independently of the PAM matrix) (-x)

frameshift (Integer)
Penalty for frameshift between codon (fast[xy]/tfast[xy])(-h)

frameshift_within (Integer)
Penalty for frameshift within a codon (fasty/tfasty)(-j)

threeframe (Switch)
Search only the three forward frames (tfasta) (-3)

invert (Switch)
Reverse complement the query sequence (all tfasta) (-i)

genetic_code (Excl)
Use genetic code for translation (tfasta/tfast[xy]/fast[xy]) (-t)

band (Integer)
band-width used for optimization (-y)

swalig (Switch)
unlimited Smith-Waterman alignment for DNA (-A)

noopt (Switch)
no limited optimization (-o)

stat (Excl)
Specify statistical calculation. (-z)

random (Switch)
Estimate stat parameters from shuffled copies of each library sequence (-z)

histogram (Switch)
No histogram (-H)

scores (Integer)
number of similarity scores to be shown (-b)

alns (Integer)
number of alignments to be shown (-d)

html_output (Switch)
HTML output (-m)

markx (Excl)
Alternate display of matches and mismatches in alignments

init1 (Switch)
sequences ranked by the z-score based on the init1 score (-1)

z_score_out (Excl)
Show normalize score as (-B)

showall (Switch)
both sequences are shown in their entirety in alignments (fasta only) (-a)

linlen (Integer)
output line length for sequence alignments (max. 200) (-w)

offsets (String)
Start numbering the aligned sequences at position x1 x2 (2 numbers) (-X)

info (Switch)
Display more information about the library sequence in the alignment (-L)

statfile (OutFile)
Write out the sequence identifier, superfamily number, and similarity scores to this file (-R)

filter (Switch)
Lower case filtering (-S)

outfile (OutFile)
pipe: mview_input

html_outfile (OutFile)