Free 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

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.

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.

Local Data Manager (LDM) is a collection of cooperating programs that select, capture, manage, and distribute arbitrary data products.
The system is designed for event-driven data distribution, and is currently used in the Unidata Internet Data Distribution (IDD) project. The LDM system includes network client and server programs and their shared protocols.
An important characteristic of the LDM is its support for flexible, site-specific configuration.
Enhancements:
- Fixes for timestamp bugs.

Bio::AlignIO::msf is a Perl module with msf sequence input/output stream.

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class.

This object can transform Bio::Align::AlignI objects to and from msf flat file databases.

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_aln

Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream. Tries to read *all* MSF
It reads all non whitespace characters in the alignment
area. For MSFs with weird gaps (eg ~~~) map them by using
$al->map_chars(~,-)
Returns : L< Bio::Align::AlignI > object
Args : NONE

write_aln

Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in MSF format
Sequence type of the alignment is determined by the first sequence.
Returns : 1 for success and 0 for error
Args : L< Bio::Align::AlignI > object

uplocalserver is a service menu which you can copy a file on your local server.

At the and youll have the file on the server and a direct link to it in the clipboard. If you want you can also change the name on the local server.

Bio::AlignIO::bl2seq is a bl2seq sequence input/output stream.

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class, as in:

use Bio::AlignIO;

$in = Bio::AlignIO->new(-file => "inputfilename" , -format => bl2seq);
$aln = $in->next_aln();

This object can create Bio::SimpleAlign sequence alignment objects (of 2 sequences) from bl2seq BLAST reports.

A nice feature of this module is that- in combination with StandAloneBlast.pm or remote blasting - it can be used to align 2 sequences and make a SimpleAlign object from them which can then be manipulated using any SimpleAlign.pm methods, eg:

#Get 2 sequences
$str = Bio::SeqIO->new(-file=>t/amino.fa , -format => Fasta, );
my $seq3 = $str->next_seq();
my $seq4 = $str->next_seq();

# Run bl2seq on them
$factory = Bio::Tools::StandAloneBlast->new(program => blastp,
outfile => bl2seq.out);
my $bl2seq_report = $factory->bl2seq($seq3, $seq4);

# Use AlignIO.pm to create a SimpleAlign object from the bl2seq report
$str = Bio::AlignIO->new(-file=> bl2seq.out,-format => bl2seq);
$aln = $str->next_aln();

local-remote-controll-gui is a Lazarus/(freepascal) programmed software for running commands on remote "server" or machine, true a file shearing.(like sshfs..)... some customize options, GUI on the user/machine...linux ppc and linux x86, the source binary enabled.