Free basic local alignment software for linux

Basic Local Alignment Search Tool is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA.
It uses a heuristic algorithm which seeks local as opposed to global alignments, and is therefore able to detect relationships among sequences which share only isolated regions of similarity.
It can be run locally as a full executable, and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. It runs on Mac OS, Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP- UX systems.
Main features:
Nucleotide
- Quickly search for highly similar sequences (megablast)
- Quickly search for divergent sequences (discontiguous megablast)
- Nucleotide-nucleotide BLAST (blastn)
- Search for short, nearly exact matches
- Search trace archives with megablast or discontiguous megablast
Protein
- Protein-protein BLAST (blastp)
- Position-specific iterated and pattern-hit initiated BLAST (PSI- and PHI-BLAST)
- Search for short, nearly exact matches
- Search the conserved domain database (rpsblast)
- Protein homology by domain architecture (cdart)
Translated
- Translated query vs. protein database (blastx)
- Protein query vs. translated database (tblastn)
- Translated query vs. translated database (tblastx)
Genomes
- Human, mouse, rat, chimp cow, pig, dog, sheep, cat
- Chicken, puffer fish, zebrafish
- Environmental samples
- Protozoa
- Insects, nematodes, plants, fungi, microbial genomes, other eukaryotic genomes
Special
- Search for gene expression data (GEO BLAST)
- Align two sequences (bl2seq)
- Screen for vector contamination (VecScreen)
- Immunoglobin BLAST (IgBlast)
- SNP BLAST
Meta
- Retrieve results

Read Local Lyrics is a little Python script works as a lyrics plugin.

If to some audio file, a corresponding ".txt" file can be found in the same folder, this is taken as the lyrics of the song.

SLAD is a tool for performing local security checks against GNU/Linux systems.

SLAD has been primarily developed for the BOSS project to work together with Nessus to enhance its local scanning capabilities. For example, scanning for weak passwords with a tool like John-the-Ripper is something that simply cannot be achieved by a network scan.

Therefore, SLAD is required to be installed on every GNU/Linux system where local auditing needs to be done. SLAD can then be used as a stand-alone application or more conveniently through Nessus. For usage with Nessus two NASL plugins are provided for interfacing between Nessus and SLAD

The Version 2.0 provides a XML Interface for Parameters and easy integration of additional audit-parameters and tools. To help the administrator to integrate a new feature-set, a development-documentation is provided with the cvs.

SLAD has been tested and verified on the following platforms:

RedHat Fedora Core 3
SuSe 9.2
Debian 3.0 (woody)
Debian 3.1 (sarge)
ERPOSS3
Gentoo Linux 2004.3

SLAD is implemented in Perl and provides an extendable plugin architecture allowing to use various GPL-based security scanners and auditing tools under one common framework. Currently, SLAD comes packaged with

John-the-Ripper
Chkrootkit
LSOF
ClamAV
Tripwire
TIGER

As a result SLAD delivers reports of these locally installed auditing and analysis tools. When used with Nessus the individual reports are wrapped into a standard Nessus report.

SLAD as well as the SLAD NASL Plugins can be downloaded from this Website in their current stable release V2.0.

Installation:

You can use our "easy-to-use" GTK installer, this installer downloads the lastest SLAD Release Binary, and install it on the target system. You only need to provide the login for the traget system.

nautilus-open-terminal project is a nautilus plugin for opening terminals in arbitrary local paths through nautilus.

Local Area Security is a research group focused on information security related subjects. We are most known for L.A.S. Linux. Our live-CD security toolkit.

Local Area Security is a project that was started in 2002 to research information security related topics. During that time there was no real live-CD toolkit focused on information security.

So Jascha, the project founder built one from a stripped down version of Knoppix called Model-K. Both of which were built from Debian Linux.

Up until version 0.4 L.A.S. Linux was command line only. Which made it limited to some of the tools it could contain since many require a GUI. Or at least for many it is preferable to have one. So FluxBox was added as the desktop since it is light weight and very feature filled.

It was during this time that Jascha came up with the idea of keeping the size of L.A.S. as small as possible, which lead to a target maximum size of 180MBs. The size of the original mini-CDs that were available at the time. This forced the selection of tools and features to be weighed heavily since unlike other live-CDs that throw in everything including the kitchen sink. L.A.S. was designed from the ground up to be a tool not a all-inclusive grab bag of applications.

As well as many advances for live-CDs came about, such as to-ram that allows booting a live-CD into the physical RAM of a computer. Which by chance L.A.S. was perfectly cut out for. With as little as 256MB of RAM people could boot L.A.S. and then free up their CD-ROMs for burring etc.

For forensics this was a big plus, along with many other uses. Plus L.A.S. ran very fast in RAM which helped with running Nessus, Nmap, or other tools. When compared to full size (700MB) CDs which would require 1GB of RAM to use the to-ram option, it was really no contest.

CBM BASIC Lister is a Commodore related application to convert BASIC programs from their binary form to text.
CBM BASIC Lister (formerly C64 BASIC Lister) is a tool to generate an easily readable and printable BASIC listing of any CBM BASIC program (C64/VIC20, etc.) saved as "prg" file.
It is not a BASIC interpreter, its not a debugger and neither a development tool. Its just a LISTer and, by default, it acts just as the C64 native "LIST" command does.
Extra flow-control options were introduced to automatically correct the aspect of each listing and format it before introducing any part of it in your own electronic documents.
Of course, it can be used to study a BASIC program listing from your PC too.
Main features:
- Optional indent-ation of cycle (and procedure with Extended sets) body, with nested cycles processing
- Optional right alignment of BASIC line numbers
- Optional blank line insertion after a RETURN/END command (and End of procedures with Extended sets)
- Simons BASIC, Ultra BASIC (ABACUS), and Special BASIC support (with detection)

Basic Ipchains Firewall Rule Script is an iptables firewall script.

WARNING THIS SCRIPT HAS NOT BEEN TESTED YET! USE AT YOUR OWN RISK.

TIPS:

- To test your ruleset without actually changing the firewall, you can change the IPTABLES variable below to "echo" and run the script. This will print a copy of the ruleset commands out to stdout (screen)

- To tidy it up even more, you could try this when you run the script with the "echo" setting:

/etc/rc.d/rc.firewall | grep ^- | sed s/^-/ipchains -/

- Or to create a prebuilt ruleset with your variables already set:

/etc/rc.d/rc.firewall | grep ^- | sed s/^-/ipchains -/ > newfile

Of course you will have to rerun this and create a new script whenever you change the variables in this script.