Free 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

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

GnoTime provides a to-do list organizer and project timer.
GnoTime is a to-do list tracker and project timer with a built-in invoice generator. It allows users to keep track of how much time they have spent working on particular tasks, maintain a diary of that work, and create invoices with task-specific billing fees and rates.
Main features:
- Multiple To-Do Lists that can be sorted by the priority/importance of the tasks in the list. The to-do items can be organized into categories, arranged in a hierarchical way. This makes it easy to maintain both business and personal items in the list, or handle many different projects, while keeping them separate from each other.
- A pair of Diary/Journal areas that can be used to keep long and detailed notes and diary entries. The project description area allows a multi-paragraph description or status to be typed in. The diary area allows day-to-day notes to be associated with a set of timestamps, so that one has a record of what one did on any given day.
- A Running Timer, with time totals, for each project/task. One starts the timer by clicking on a task: it will measure the amount of time that you are in front of the computer. If it detects that the keyboard/mouse are idle, it will stop the clock. If the clock stays stopped too long, it will nag you to start it up again. You can view time totals by day, week, month or year.
- A Billing Status dialog for each diary entry. You can mark any given diary entry as bill-able/non-bill-able, paid or pending, and set the billing rate. Each project can also be marked up with a set of project-planning information: planed start, end and due dates, hours to finish, percent-complete. This is in addition to assigning an urgency/importance to each project, as well as a status (completed/in-progress not-started/canceled).
- A half-dozen different HTML Reports that can slice and dice your lists. Theres a Journal report that shows all of the diary entries for one given project. Theres an Invoice report that summarizes the time spent on each entry, and computes a dollar amount for it. Theres a Status Report that prints the title of each project, together with the paragraph-long descriptions of each. Theres a ToDo report, which prints only the project title, the importance/urgency, and the completed/in-progress/not-started status. The Daily report summarizes the total time spent on a day-by-day basis, and lists each of the projects that were worked on in a given day. Each of these reports can be customized. And, because theyre HTML, you can even publish them as web pages. (Yes, Ive thought of using GnoTime as a weblog management/publishing tool).
Enhancements:
- Build against QOF version 0.6.0, if available.
- Fix issue where yelp doesnt display an entry for gnotime when browsing because it doesnt recognize the entry
- Fix sourceforge bug [ 799077 ] projects blanked when first time user tries to sort
- fix broken leap-year calculation, leading to bugs sourceforge bugs [ 983408 ] and [ 1114205 ]
- Fix crash due to hoverhelp timer popping after a report window is closed.
- Change activity report to display date/time in two distinct html table columns (prettier alignment)
- Bug fix: sourceforge bug report fixed [ 877193 ] toolbar wont go to/stay in text-only mode
- Bug fix: editing time brings up wrong report
- fedora .spec file is out of date and rpm cannot build rpm
- Fix bug involving copy of old gnotime files to a new machine on which gnotime has never been run before.
- Fix sourceforge bug [ 1276458 ] "Empty" appears in diary entry
- Apply sourceforge patch 1176719 Extensible fix for gtkhtml3 building
- Apply 1171394 Adds separate timeout for "No Project" dialog
- Apply sourceforge patch 085911 Add "-" value for status field
- Apply sourceforge patch 074658 Add wordwrapping to diary entry boxes
- Apply sourceforge patch 1074458 Fix a crash when invoking help
- Apply sourceforge patch 1038701 Fix to Activity item in popup menu
- Apply sourceforge patch 1027582 Build system update for qof inclusion
- Fix idle time so that it works with Linux 2.6 kernel /proc/interrupts
- use %e to see the estimated sizing of a project in the logfiles
- Apply new pt_BR translation from Goedson Teixeira Paixao
- Fix for Debian Bug #250776, change widget visibility in the edit interval dialog

Bio::Tools::AlignFactory is a base object for alignment factories.

SYNOPSIS

You wont be using this as an object, but using a dervied class like Bio::Tools::pSW

Holds common Alignment Factory attributes in place

Xmame is the X11/Unix port of MAME. MAME is the Multiple Arcade Machine Emulator, an arcade (coin-op) video game emulator.
The latest stable release is capable of playing over 2000 arcade games.
Enhancements:
- Everything from MAME 0.106 (changes-mame.html) and MESS 0.106 (changes-mess.html).
- Reverted a change that was intended to work around some Metacity focus misbehavior but was causing all window managers to have focus problems in fullscreen mode.
- Fixed a link error for messtest. (Arnaud G. Gibert)
- The clean68k target now removes libcpu.a, which fixes link errors for successive builds made without a full clean. (Arnaud G. Gibert)
- Fixed an alignment bug in the OpenGL driver which caused Defender, and possibly other 16bpp games, to be skewed.
- The mouse is no longer automatically grabbed in fullscreen mode. Bugzilla bug 877.
- Replaced fuzzy game name comparison with the method used by MAME for Windows, which lists approximate matches when an exact match isnt found.
- A BadMatch error should no longer occur for the OpenGL target in some cases, such as when 16bpp mode is used with recent releases of the binary NVIDIA driver.
- Fixed the tiny build target. (Mike Frysinger)
- Added CFLAGS for the Blackfin CPU. (Mike Frysinger)
- BUILD_ZLIB and BUILD_EXPAT can now be disabled without having to edit the makefile. (Mike Frysinger)

HPC Challenge is a high performance benchmark suite. The HPC Challenge consists of basically 7 benchmarks:
1. HPL - the Linpack TPP benchmark which measures the floating point rate of execution for solving a linear system of equations.
2. DGEMM - measures the floating point rate of execution of double precision real matrix-matrix multiplication.
3. STREAM - a simple synthetic benchmark program that measures sustainable memory bandwidth (in GB/s) and the corresponding computation rate for simple vector kernel.
4. PTRANS (parallel matrix transpose) - exercises the communications where pairs of processors communicate with each other simultaneously. It is a useful test of the total communications capacity of the network.
5. RandomAccess - measures the rate of integer random updates of memory (GUPS).
6. FFTE - measures the floating point rate of execution of double precision complex one-dimensional Discrete Fourier Transform (DFT).
7. Communication bandwidth and latency - a set of tests to measure latency and bandwidth of a number of simultaneous communication patterns; based on b_eff (effective bandwidth benchmark).
Compiling:
The first step is to create a configuration file that reflects characteristics of your machine. The configuration file should be created in the hpl directory. This directory contains instructions (the files README and INSTALL) on how to create the configuration file. The directory hpl/setup contains many examples of configuration files. A good approach is to copy one of them to the hpl directory and if it doesnt work then change it. This file is reused by all the components of the HPC Challange suite.
When configuration is done, a file should exist in the hpl directory whose name starts with Make. and ends with the name for the system used for tests. For example, if the name of the system is Unix, the file should be named Make.Unix.
To build the benchmark executable (for the system named Unix) type: make arch=Unix. This command should be run in the top directory (not in the hpl directory). It will look in the hpl directory for the configuration file and use it to build the benchmark executable.
Configuration:
The HPC Challange is driven by a short input file named hpccinf.txt that is almost the same as the input file for HPL (customarily called HPL.dat). Refer to the file hpl/www/tuning.html for details about the input file for HPL. A sample input file is included with the HPC Challange distribution.
The differences between HPL input file and HPC Challange input file can be summarized as follows:
- Lines 3 and 4 are ignored. The output always goes to the file named hpccoutf.txt.
- There are additional lines (starting with line 33) that may (but do not have to) be used to customize the HPC Challenge benchmark. They are described below.
The additional lines in the HPC Challenge input file (compared to the HPL input file) are:
Lines 33 and 34 describe additional matrix sizes to be used for running the PTRANS benchmark (one of the components of the HPC Challange benchmark).
- Lines 35 and 36 describe additional blocking factors to be used for running PTRANS benchmark.
Just for completeness, here is the list of lines of the HPC Challanges input file with brief descriptions of their meaning:
- Line 1: ignored
- Line 2: ignored
- Line 3: ignored
- Line 4: ignored
- Line 5: number of matrix sizes for HPL (and PTRANS)
- Line 6: matrix sizes for HPL (and PTRANS)
- Line 7: number of blocking factors for HPL (and PTRANS)
- Line 8: blocking factors for HPL (and PTRANS)
- Line 9: type of process ordering for HPL
- Line 10: number of process grids for HPL (and PTRANS)
- Line 11: numbers of process rows of each process grid for HPL (and
PTRANS)
- Line 12: numbers of process columns of each process grid for HPL
(and PTRANS)
- Line 13: threshold value not to be exceeded by scaled residual for
HPL (and PTRANS)
- Line 14: number of panel factorization methods for HPL
- Line 15: panel factorization methods for HPL
- Line 16: number of recursive stopping criteria for HPL
- Line 17: recursive stopping criteria for HPL
- Line 18: number of recursion panel counts for HPL
- Line 19: recursion panel counts for HPL
- Line 20: number of recursive panel factorization methods for HPL
- Line 21: recursive panel factorization methods for HPL
- Line 22: number of broadcast methods for HPL
- Line 23: broadcast methods for HPL
- Line 24: number of look-ahead depths for HPL
- Line 25: look-ahead depths for HPL
- Line 26: swap methods for HPL
- Line 27: swapping threshold for HPL
- Line 28: form of L1 for HPL
- Line 29: form of U for HPL
- Line 30: value that specifies whether equilibration should be used
by HPL
- Line 31: memory alignment for HPL
- Line 32: ignored
- Line 33: number of additional problem sizes for PTRANS
- Line 34: additional problem sizes for PTRANS
- Line 35: number of additional blocking factors for PTRANS
- Line 36: additional blocking factors for PTRANS
Enhancements:
- This version contains many bugfixes, major features, and minor enhancements, many of which were contributed by users.
- The major focus of this release was to improve accuracy of the reported performance results and ensure scalability of the code on the largest supercomputer installations with hundreds of thousands of computational cores.

karamTop is a superkaramba theme that parses /proc. Shows an X number of running processes with CPU, Memory usage and program name, sorted by CPU. The default number of processes to show is 5.
Idea based on the gkrelltop a plugin for GKrellM. pytop.py is the core class file. It can be used within any kind of script.
Keep in mind since it reads /proc directly, this means its Linux only. As FreeBSD and possibly other *nixes have a completely different /proc layout.
The GUI configuration isnt that great. There isnt much error checking. You can always modify the theme configuration files for fine tuning. Any more options and it just becomes too tedious to code. Right click on Karamtop, Configure Theme:
- Choose Theme
- Whether to hide processes with a cpu percent of 0
- Set the alignment for the command (program name) text
- Set the column order of the output
For theme creaters. The theme layout is designed so you can create a directory inside of the theme directory with the name of your theme. Which will contain the configuration file and images. That way you can tar up everything easily. This wont work with the skz format. I suppose maybe Ill make something that will automatically install themes in tar.gz format at some point.
Designed to work with my theme, MiniKaramba. http://www.kde-look.org/content/show.php?content=27802
A karamtop theme with an alternative background: http://www.kde-look.org/content/show.php?content=25626
Work like this is encouraged. Thanks.
Enhancements:
- Sometimes karamtop/superkaramba would run for weeks without crashing and other times it would crash relatively soon.
- Now karamtop defaults with threading off, but supports turning it back on through the config.