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BottomFeeder 4.4
BottomFeeder is a viewer for RSS feeds. more>>
BottomFeeder is a news aggregator client for RSS and Atom feeds, written in VisualWorks Smalltalk. BottomFeeder runs on x86 Linux (also FreeBSD), PowerPC linux, Sparc Linux, Windows (98/ME/NT/2000/XP), Mac OS8/9, Mac OS X, AIX, SGI Irix, Compaq UNIX, HP-UX, and Solaris.
Main features:
- Full support for CSS, including user defined CSS
- View news in 3 pane or 2 pane modes
- Subscribe to any RSS or Atom format in use
- View items in a summary Newspaper View
- Synchronize 2 or more BottomFeeders via HTTP or file import
- Subscribe to feeds or feedlists
- Supports HTTPS, HTTP Authentication, and HTTP Digest Authentication
- Plugins for blogging, IRC, and MSN Messenger contacts
- Easy to update or upgrade from within BottomFeeder
- Save as many or as few feed items for as long as you want
- Import or Export in common OPML format
- Binary compatible on every platform. No need to recompile
Enhancements:
- The Feedlists folder has been eliminated.
- Importing a feedlist now adds feeds directly to your subscription list.
- The separate "Searches" folder has been eliminated.
- Search feeds are now part of your subscription list, and are marked with a new icon.
- Tabs now open empty and remember their previous state.
- There are many other changes and enhancements.
<<lessMain features:
- Full support for CSS, including user defined CSS
- View news in 3 pane or 2 pane modes
- Subscribe to any RSS or Atom format in use
- View items in a summary Newspaper View
- Synchronize 2 or more BottomFeeders via HTTP or file import
- Subscribe to feeds or feedlists
- Supports HTTPS, HTTP Authentication, and HTTP Digest Authentication
- Plugins for blogging, IRC, and MSN Messenger contacts
- Easy to update or upgrade from within BottomFeeder
- Save as many or as few feed items for as long as you want
- Import or Export in common OPML format
- Binary compatible on every platform. No need to recompile
Enhancements:
- The Feedlists folder has been eliminated.
- Importing a feedlist now adds feeds directly to your subscription list.
- The separate "Searches" folder has been eliminated.
- Search feeds are now part of your subscription list, and are marked with a new icon.
- Tabs now open empty and remember their previous state.
- There are many other changes and enhancements.
Download (2.3MB)
Added: 2007-07-10 License: Artistic License Price:
2046 downloads

BottomFeeder for Solaris 4.4
BottomFeeder is a news aggregator client written in VisualWorks Smalltalk more>> BottomFeeder is a news aggregator client (RSS and Atom) written in VisualWorks Smalltalk. BottomFeeder runs on Linux x86, (also FreeBSD), PowerPC Linux, Sparc Linux, Windows (98/ME/NT/2000/XP/CE 4), Mac OS8/9, Mac OS X (PPC, intel), AIX, SGI Irix, HP-UX, and Solaris (SPARC and x86).
What sets BottomFeeder apart?
Full support for CSS, including user defined CSS
View news in 3 pane or 2 pane modes
Subscribe to any RSS or Atom format in use
View items in a summary Newspaper View
Synchronize 2 or more BottomFeeders via HTTP or file import
Subscribe to feeds or feedlists
Supports HTTPS, HTTP Authentication, and HTTP Digest Authentication
Plugins for blogging, IRC, and MSN Messenger contacts
Easy to update or upgrade from within BottomFeeder
Save as many or as few feed items for as long as you want
Import or Export in common OPML format
Binary compatible on every platform. No need to recompile<<less
Download (16.7MB)
Added: 2009-04-28 License: Freeware Price: Free
178 downloads

BottomFeeder for Solaris x86 4.4
BottomFeeder is a news aggregator client written in VisualWorks Smalltalk more>> BottomFeeder is a news aggregator client (RSS and Atom) written in VisualWorks Smalltalk. BottomFeeder runs on Linux x86, (also FreeBSD), PowerPC Linux, Sparc Linux, Windows (98/ME/NT/2000/XP/CE 4), Mac OS8/9, Mac OS X (PPC, intel), AIX, SGI Irix, HP-UX, and Solaris (SPARC and x86).
What sets BottomFeeder apart?
Full support for CSS, including user defined CSS
View news in 3 pane or 2 pane modes
Subscribe to any RSS or Atom format in use
View items in a summary Newspaper View
Synchronize 2 or more BottomFeeders via HTTP or file import
Subscribe to feeds or feedlists
Supports HTTPS, HTTP Authentication, and HTTP Digest Authentication
Plugins for blogging, IRC, and MSN Messenger contacts
Easy to update or upgrade from within BottomFeeder
Save as many or as few feed items for as long as you want
Import or Export in common OPML format
Binary compatible on every platform. No need to recompile<<less
Download (16.3MB)
Added: 2009-04-29 License: Freeware Price: Free
183 downloads

BottomFeeder for Intel Linux 4.4
BottomFeeder is a news aggregator client written in VisualWorks Smalltalk more>> BottomFeeder is a news aggregator client (RSS and Atom) written in VisualWorks Smalltalk. BottomFeeder runs on Linux x86, (also FreeBSD), PowerPC Linux, Sparc Linux, Windows (98/ME/NT/2000/XP/CE 4), Mac OS8/9, Mac OS X (PPC, intel), AIX, SGI Irix, HP-UX, and Solaris (SPARC and x86).
What sets BottomFeeder apart?
Full support for CSS, including user defined CSS
View news in 3 pane or 2 pane modes
Subscribe to any RSS or Atom format in use
View items in a summary Newspaper View
Synchronize 2 or more BottomFeeders via HTTP or file import
Subscribe to feeds or feedlists
Supports HTTPS, HTTP Authentication, and HTTP Digest Authentication
Plugins for blogging, IRC, and MSN Messenger contacts
Easy to update or upgrade from within BottomFeeder
Save as many or as few feed items for as long as you want
Import or Export in common OPML format
Binary compatible on every platform. No need to recompile<<less
Download (16.2MB)
Added: 2009-04-26 License: Freeware Price: Free
180 downloads
Games::WoW::PVP 0.01
Games::WoW::PVP is a Perl module with the great new Games::WoW::PVP! more>>
Games::WoW::PVP is a Perl module with the great new Games::WoW::PVP!
SYNOPSIS
Quick summary of what the module does.
Perhaps a little code snippet.
use Games::WoW::PVP;
my $WoW = Games::WoW::PVP->new();
# looking for a character
my %hash = $WoW->search_player(
{ country => EU, # EU europe US us
realm => conseil des ombres, # name of the realm
faction => h, # h horde a ally
character => raspa, # name of the player
}
);
# looking for top players
my %hash = $WoW->top(
{ country => EUR,
realm => elune,
faction => a,
}
);
<<lessSYNOPSIS
Quick summary of what the module does.
Perhaps a little code snippet.
use Games::WoW::PVP;
my $WoW = Games::WoW::PVP->new();
# looking for a character
my %hash = $WoW->search_player(
{ country => EU, # EU europe US us
realm => conseil des ombres, # name of the realm
faction => h, # h horde a ally
character => raspa, # name of the player
}
);
# looking for top players
my %hash = $WoW->top(
{ country => EUR,
realm => elune,
faction => a,
}
);
Download (0.004MB)
Added: 2007-01-05 License: Perl Artistic License Price:
1025 downloads
BetaFTPD 0.0.8-pre17
BetaFTPD provides a single-threaded, small FTP daemon. more>>
BetaFTPD provides a single-threaded, small FTP daemon.
BetaFTPD is a single-threaded FTP daemon. The single-threadedness makes it faster than most other FTP daemons (contrary to common belief), and makes it extremely light on memory.
Although it lacks a few functions (which you probably wont miss), the current version is very small and has a decent amount of functionality.
BetaFTPD is built on the concept of heavy code reuse, which should hopefully make it easier for other programmers to contribute.
Enhancements:
- Support for not running as root.
- Fixed a LOT of bugs, some segfaulting, some minor.
- MAJOR performance improvements in almost all areas.
- Some changes to compile better under Debian GNU/Linux, a debian/ directory, and .deb files available for download.
- BetaFTPD will now try to install itself (wow! (not)) in the same directory as the file called `ftpd, if you have that file.
- Support for non-Linux platforms! For now, only SunOS/SVR4 and FreeBSD.
- Gave the version its own name, like Samba does.
<<lessBetaFTPD is a single-threaded FTP daemon. The single-threadedness makes it faster than most other FTP daemons (contrary to common belief), and makes it extremely light on memory.
Although it lacks a few functions (which you probably wont miss), the current version is very small and has a decent amount of functionality.
BetaFTPD is built on the concept of heavy code reuse, which should hopefully make it easier for other programmers to contribute.
Enhancements:
- Support for not running as root.
- Fixed a LOT of bugs, some segfaulting, some minor.
- MAJOR performance improvements in almost all areas.
- Some changes to compile better under Debian GNU/Linux, a debian/ directory, and .deb files available for download.
- BetaFTPD will now try to install itself (wow! (not)) in the same directory as the file called `ftpd, if you have that file.
- Support for non-Linux platforms! For now, only SunOS/SVR4 and FreeBSD.
- Gave the version its own name, like Samba does.
Download (0.083MB)
Added: 2007-04-30 License: GPL (GNU General Public License) Price:
907 downloads
iLeech 0.10
iLeech is a Mac OS X application that will connect to an iTunes 4.0. more>>
iLeech is a Mac OS X application that will connect to an iTunes 4.0. Introduced in iTunes v4.0 is the ability to share your playlist with other iTunes users.
This is accomplished locally using Rendezvous/zeroconf/mdns/whatever, or if you know the IP address of a machine you can access its playlist via daap:// (provided port 3689 is open). However, you can only stream the music from the iTunes host -- no copies are made on your machine.
iLeech will connect to an iTunes host, display their playlist, and allow you to copy the files to your local drive. It can be downloaded by clicking the "Download" button from the navigation bar.
And all I can say is "Wow". In my wildest dreams I would not have imagined the reaction/attention my simple little Java/Cocoa application would receive. When I initially released it, I had honestly never imagined more than a couple of dozen people would be interested in it. Call me naive if you will, but that is the truth on my end. But that idea has certainly been shattered during the past week, as in the first 4 days the page received an overwhelming 9,399 page views (and 2,147 downloads)
<<lessThis is accomplished locally using Rendezvous/zeroconf/mdns/whatever, or if you know the IP address of a machine you can access its playlist via daap:// (provided port 3689 is open). However, you can only stream the music from the iTunes host -- no copies are made on your machine.
iLeech will connect to an iTunes host, display their playlist, and allow you to copy the files to your local drive. It can be downloaded by clicking the "Download" button from the navigation bar.
And all I can say is "Wow". In my wildest dreams I would not have imagined the reaction/attention my simple little Java/Cocoa application would receive. When I initially released it, I had honestly never imagined more than a couple of dozen people would be interested in it. Call me naive if you will, but that is the truth on my end. But that idea has certainly been shattered during the past week, as in the first 4 days the page received an overwhelming 9,399 page views (and 2,147 downloads)
Download (0.055MB)
Added: 2006-07-20 License: LGPL (GNU Lesser General Public License) Price:
1191 downloads
RPilot 1.4.2
RPilot project is an interpreter for the IEEE-standard language PILOT. more>>
RPilot project is an interpreter for the IEEE-standard language PILOT.
RPilot is an interpreter for the IEEE-standard programming language PILOT written in portable C.
PILOT is a language that was designed in the 1960s to support computer-aided instruction and is very simple to learn.
RPilot comes with an introduction to the language and several examples.
Enhancements:
- Fix usage of `isblank(), a GNU extension (Thanks to Patrick Eaton)
- Add some #defines to rpilot.h to replace a few hard-coded constants
- RPilot is over 4 years old. Wow.
<<lessRPilot is an interpreter for the IEEE-standard programming language PILOT written in portable C.
PILOT is a language that was designed in the 1960s to support computer-aided instruction and is very simple to learn.
RPilot comes with an introduction to the language and several examples.
Enhancements:
- Fix usage of `isblank(), a GNU extension (Thanks to Patrick Eaton)
- Add some #defines to rpilot.h to replace a few hard-coded constants
- RPilot is over 4 years old. Wow.
Download (0.036MB)
Added: 2006-11-02 License: GPL (GNU General Public License) Price:
1086 downloads
WheelOfFortune 0.2
WheelOfFortune is a HIGHLY experimental but fascinating superkaramba enhancement. more>>
WheelOfFortune is a HIGHLY experimental but fascinating superkaramba enhancement, with an example theme to see the principle and also a work-in-progress theme.
Wheel smoothly your way through your files without having to spend all your time clicking on folders.
The enhancements: listing file and directories in Superkaramba - but its a bit more than that: KDirlister is used, which supports application:/, file:/, floppy:/ media:/ devices:/ svn:/ in fact any KIO.
I am so bowled over by how exciting and how... "wow!" this is that i just had to let people know about it.
Try the wof.theme and you will see what i mean.
If you have a mouse with a scroll-wheel, use it: its much easier to navigate. single-click on a directory to open it up on the arc below (yes, its a wheel, not a line, not a square, not a treeview!)
The download contains:
- a precompiled superkaramba binary
- a superkaramba diff (patch)
- the dirlister.cpp and .h files
- an example theme (dirlister)
- a work-in-progress theme (wof).
Enhancements:
- fixed large subdirectory crash
- added "run" capability properly
<<lessWheel smoothly your way through your files without having to spend all your time clicking on folders.
The enhancements: listing file and directories in Superkaramba - but its a bit more than that: KDirlister is used, which supports application:/, file:/, floppy:/ media:/ devices:/ svn:/ in fact any KIO.
I am so bowled over by how exciting and how... "wow!" this is that i just had to let people know about it.
Try the wof.theme and you will see what i mean.
If you have a mouse with a scroll-wheel, use it: its much easier to navigate. single-click on a directory to open it up on the arc below (yes, its a wheel, not a line, not a square, not a treeview!)
The download contains:
- a precompiled superkaramba binary
- a superkaramba diff (patch)
- the dirlister.cpp and .h files
- an example theme (dirlister)
- a work-in-progress theme (wof).
Enhancements:
- fixed large subdirectory crash
- added "run" capability properly
Download (0.22MB)
Added: 2006-06-29 License: GPL (GNU General Public License) Price:
1212 downloads
WoW Companion 0.2.8
WoW Companion is a Java client/server used to centrally store character, item, and other data for World of Warcraft. more>>
WoW Companion is a Java client and server used to centrally store item, character and other data for World of Warcraft.
Data is made available via the Web in XML and other formats. Frontends for displaying character profiles are also included.
<<lessData is made available via the Web in XML and other formats. Frontends for displaying character profiles are also included.
Download (0.67MB)
Added: 2006-01-10 License: GPL (GNU General Public License) Price:
1391 downloads
GUMP 1.0
GUMP script works on the LAB channels to add rich color saturation effects to your photo. more>>
GUMP script works on the LAB channels to add rich color saturation effects to your photo. This is the twin sister script of Photo LAB WoW !!
The latest version at source forge archive allows you to do cool color changes, including black and white conversion.
<<lessThe latest version at source forge archive allows you to do cool color changes, including black and white conversion.
Download (MB)
Added: 2006-09-20 License: GPL (GNU General Public License) Price:
656 downloads
Web Of Web 6 b07282211
Web Of Web (WoW) is a new, Structural, Secure, Collaborative and Realtime Interactive media platform for the Web. more>>
Web Of Web (WoW) is a new, Structural, Secure, Collaborative and Realtime Interactive media platform for the Web.
Structural
WoW presents a Mind Mapping alike interface, which best reflects human ideas and thinking pathes, it shall greatly help people express themselves and understand others thought.
Even further, WoW brings intellectuals of single brains into collective collaboration. It persists and funds mind sparks over time scale, and when deployed over the Internet (The default and native mode of WoW), it scales all over the world.
WoW also extends MindMapping to support physical links of ideas, thus Mind Maps are never limited to a tree structure, but possibly a interconnected information web. (This is how WoW had been named, it is the [Information Web] of the [Computer Web]).
Secure
WoW strictly enforces permission authorization by design, as well as implemented flexible identity organization and ACL mechanism. Security management interface is integrated with WoW, and is as easy to use as other daily operations. The flexibility of WoW Security also enables it simulate Wiki, BBS, BLOG, IRC and other classic web community applications easily.
WoW leverages certificates to let user decide whether to trust a WoW site, and private and sensitive data such as login id and password are always sent after strong encryption, the security is created by AES session key exchanged after RSA encryption at both side.
Collaborative
There is no obvious ownership by default, the achievement belongs to everyone ever contributed with given permissions. Information History is natively kept and available to every participants having view permissions. Even the instant talking history is kept and available for time back tracing.
Plus the realtime feature of WoW, peoples all over the world could be in close interactive collaboration at anytime, from any place.
Realtime Interactive
Creation, modification and removal of idea nodes are seen by all viewers, in realtime! The delay could be no longer than a few seconds.
Every node can be an independent talking topic, peoples could be in instant talking just inplace the focus.
Enhancements:
- The bundled TOB was upgraded to 6.0b0728.
- An interactive Java shell for dynamic management and development is available now.
<<lessStructural
WoW presents a Mind Mapping alike interface, which best reflects human ideas and thinking pathes, it shall greatly help people express themselves and understand others thought.
Even further, WoW brings intellectuals of single brains into collective collaboration. It persists and funds mind sparks over time scale, and when deployed over the Internet (The default and native mode of WoW), it scales all over the world.
WoW also extends MindMapping to support physical links of ideas, thus Mind Maps are never limited to a tree structure, but possibly a interconnected information web. (This is how WoW had been named, it is the [Information Web] of the [Computer Web]).
Secure
WoW strictly enforces permission authorization by design, as well as implemented flexible identity organization and ACL mechanism. Security management interface is integrated with WoW, and is as easy to use as other daily operations. The flexibility of WoW Security also enables it simulate Wiki, BBS, BLOG, IRC and other classic web community applications easily.
WoW leverages certificates to let user decide whether to trust a WoW site, and private and sensitive data such as login id and password are always sent after strong encryption, the security is created by AES session key exchanged after RSA encryption at both side.
Collaborative
There is no obvious ownership by default, the achievement belongs to everyone ever contributed with given permissions. Information History is natively kept and available to every participants having view permissions. Even the instant talking history is kept and available for time back tracing.
Plus the realtime feature of WoW, peoples all over the world could be in close interactive collaboration at anytime, from any place.
Realtime Interactive
Creation, modification and removal of idea nodes are seen by all viewers, in realtime! The delay could be no longer than a few seconds.
Every node can be an independent talking topic, peoples could be in instant talking just inplace the focus.
Enhancements:
- The bundled TOB was upgraded to 6.0b0728.
- An interactive Java shell for dynamic management and development is available now.
Download (MB)
Added: 2007-07-30 License: GPL (GNU General Public License) Price:
816 downloads
Exception::Class::TCF 0.03
Exception::Class::TCF is a Java/C++ style exception handling. more>>
Exception::Class::TCF is a Java/C++ style exception handling.
SYNOPSIS
try BLOCK [ [catch] NAME FUN_REF ]*
throw [ EXCEPTION LIST ]
package EnclosureException;
@ISA = qw(Exception::Class::TCF);
package main;
use Exception::Class::TCF;
try {
if ($Lost) {
throw new EnclosureException Message => "Help!";
}
else {
throw Error;
}
}
catch EnclosureException => sub {
warn "Message ",$_[0]->message," received.n"
},
Default => sub {
warn $_[0]->type, " exception ignored, trace:", $_[0]->trace
};
The Exception::Class::TCF module provides the possibility of executing a code block and specifying actions when different exceptions are raised. The try function takes as its argument a code block followed by a list of pairs of exception package names and function references, representing the action to take if a subclass of that package is raised. To increase readability the keyword catch may be inserted before any name-action pair. The return value of try is the return value of the block if no exception is thrown and the return value of the action of the chosen action in case one is found.
Even though the builtin die is used in the implementation any explicit use of die within the dynamic scope is ignored by the exception mechanism and thus works as usual. On the other hand an eval block will catch a thrown exception if it has not been caught by a try block. The clean-up routines after such a block may call throw as in the next section.
How to create an exception context.
An exception context in which thrown exceptions are handled is created using try as in
try { throw Error }
catch Default => sub { warn "Wow" };
The first argument is a code block (or a function reference). It will be referred to as a try block and any code executed inside it (including psossibly nested calls of functions in it) will be said to be in the dynamic scope of the block. After the try block follows a sequence of exception name - handling code pairs. The name will be referred to as the exception key and the corresponding code the handler (or catch handler) for that key.
An exception is either the name of a package inheriting from the package Exception::Class::TCF or an object blessed in such a package. In both cases the name of the package will be referred to as the name of the exception. All exception keys has to be names of exceptions except the special exception key Default which is the name for exceptions of package Exception::Class::TCF. In order not to clutter package name space, package names are normally prefixed by the Exception::Class::TCF:: prefix. To increase readability this prefix may be removed in exception key names and when calling throw with a package name as first argument.
The exception key may also be the string Finally. This does not correspond to an exception but instead its handler will be called just before the try function returns. Its value will be ignored however.
As new is a virtual function it can not be called with these shortened package names. For this on can use Exception::Class::TCF::make instead.
<<lessSYNOPSIS
try BLOCK [ [catch] NAME FUN_REF ]*
throw [ EXCEPTION LIST ]
package EnclosureException;
@ISA = qw(Exception::Class::TCF);
package main;
use Exception::Class::TCF;
try {
if ($Lost) {
throw new EnclosureException Message => "Help!";
}
else {
throw Error;
}
}
catch EnclosureException => sub {
warn "Message ",$_[0]->message," received.n"
},
Default => sub {
warn $_[0]->type, " exception ignored, trace:", $_[0]->trace
};
The Exception::Class::TCF module provides the possibility of executing a code block and specifying actions when different exceptions are raised. The try function takes as its argument a code block followed by a list of pairs of exception package names and function references, representing the action to take if a subclass of that package is raised. To increase readability the keyword catch may be inserted before any name-action pair. The return value of try is the return value of the block if no exception is thrown and the return value of the action of the chosen action in case one is found.
Even though the builtin die is used in the implementation any explicit use of die within the dynamic scope is ignored by the exception mechanism and thus works as usual. On the other hand an eval block will catch a thrown exception if it has not been caught by a try block. The clean-up routines after such a block may call throw as in the next section.
How to create an exception context.
An exception context in which thrown exceptions are handled is created using try as in
try { throw Error }
catch Default => sub { warn "Wow" };
The first argument is a code block (or a function reference). It will be referred to as a try block and any code executed inside it (including psossibly nested calls of functions in it) will be said to be in the dynamic scope of the block. After the try block follows a sequence of exception name - handling code pairs. The name will be referred to as the exception key and the corresponding code the handler (or catch handler) for that key.
An exception is either the name of a package inheriting from the package Exception::Class::TCF or an object blessed in such a package. In both cases the name of the package will be referred to as the name of the exception. All exception keys has to be names of exceptions except the special exception key Default which is the name for exceptions of package Exception::Class::TCF. In order not to clutter package name space, package names are normally prefixed by the Exception::Class::TCF:: prefix. To increase readability this prefix may be removed in exception key names and when calling throw with a package name as first argument.
The exception key may also be the string Finally. This does not correspond to an exception but instead its handler will be called just before the try function returns. Its value will be ignored however.
As new is a virtual function it can not be called with these shortened package names. For this on can use Exception::Class::TCF::make instead.
Download (0.011MB)
Added: 2007-06-05 License: Perl Artistic License Price:
872 downloads
NeoBio pre-alpha
NeoBio project consists of Bioinformatics algorithms in Java. more>>
NeoBio project consists of Bioinformatics algorithms in Java.
What algorithms? The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment).
Anything else? Yes, a more efficient approach, due to Crochemore, Landau and Ziv-Ukelson is also available.
It uses Lempel-Ziv compression to speed-up the computation of the dynamic programming matrix. It also relies on the SMAWK algorithm, due to Aggarwal et al., that computes all column maxima of a totally monotone matrix in linear time.
Hum... And all sequence alignment algorithms support simple scoring schemes as well as substitution matrices such as standard BLOSUM and PAM matrices. But so far they support constant gap penalty functions only.
Future versions may contain related algorithms such as multiple sequence alignment, database search and protein structure prediction.
Wow...Last but not least, NeoBio also provides a simple GUI and command line based tools to run the sequence alignment algorithms on DNA and protein sequences.
<<lessWhat algorithms? The current version consists mainly of (pairwise) sequence alignment algorithms such as the classical dynamic programming methods of Needleman & Wunsch (global alignment) and Smith & Waterman (local alignment).
Anything else? Yes, a more efficient approach, due to Crochemore, Landau and Ziv-Ukelson is also available.
It uses Lempel-Ziv compression to speed-up the computation of the dynamic programming matrix. It also relies on the SMAWK algorithm, due to Aggarwal et al., that computes all column maxima of a totally monotone matrix in linear time.
Hum... And all sequence alignment algorithms support simple scoring schemes as well as substitution matrices such as standard BLOSUM and PAM matrices. But so far they support constant gap penalty functions only.
Future versions may contain related algorithms such as multiple sequence alignment, database search and protein structure prediction.
Wow...Last but not least, NeoBio also provides a simple GUI and command line based tools to run the sequence alignment algorithms on DNA and protein sequences.
Download (0.10MB)
Added: 2006-10-30 License: GPL (GNU General Public License) Price:
1091 downloads
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