Free to determine software for linux

Devel::Profile is a Perl module to tell me why my perl program runs so slowly.

SYNOPSIS

perl -d:Profile program.pl
less prof.out

The Devel::Profile package is a Perl code profiler. This will collect information on the execution time of a Perl script and of the subs in that script. This information can be used to determine which subroutines are using the most time and which subroutines are being called most often.
To profile a Perl script, run the perl interpreter with the -d debugging switch. The profiler uses the debugging hooks. So to profile script test.pl the following command should be used:

perl -d:Profile test.pl

When the script terminates (or periodicly while running, see ENVIRONMENT) the profiler will dump the profile information to a file called prof.out. This file is human-readable, no additional tool is required to read it.

Note: Statistics are kept per sub, not per line.

SSHatter uses a brute force technique to determine the how to log into an SSH server. The project simply tries each combination in a list of usernames and passwords to determine which ones successfully log in.
Enhancements:
- Modified to allow multiple hostnames and usernames
- Added passwords (taken from http://www.nth-dimension.org.uk/downloads.php?id=30)

HTTP::BrowserDetect is a Perl module to determine the Web browser, version, and platform from an HTTP user agent string.

SYNOPSIS

use HTTP::BrowserDetect;

my $browser = new HTTP::BrowserDetect($user_agent_string);

# Detect operating system
if ($browser->windows) {
if ($browser->winnt) ...
if ($brorwser->win95) ...
}
print $browser->mac;

# Detect browser vendor and version
print $browser->netscape;
print $browser->ie;
if (browser->major(4)) {
if ($browser->minor() > .5) {
...
}
}
if ($browser->version() > 4) {
...;
}

# Process a different user agent string
$browser->user_agent($another_user_agent_string);

The HTTP::BrowserDetect object does a number of tests on an HTTP user agent string. The results of these tests are available via methods of the object.

MP3 as CD verifier 2 performs lookups on CDDB servers in an attempt to determine whether one or multiple directories of downloaded/ripped MP3 files has correct track lengths.
Please remember that mp3ascd uses the alphabetically sorted list of .mp3 files per directory Hence it is possible that if your filenames are somehow mismatched (case?), they may be sorted incorrectly. If youre getting a mismatch that you think is wrong, run mp3ascd with default options to make sure that the enumerated list of files it finds is sorted correctly.
To install, firstly make sure the script is executable.
I copy mine into a directory in my PATH, such as /usr/bin/. It should work on a multitude of platforms, but if it does not work on yours, please let me know.
Enhancements:
- Improved readability
- Summary reports (recursive), including non-matching directories
- ID3 tag presence info shown in full display mode

Tcpbroker does TCP port forwarding with a twist: it connects two incoming sockets together. Tcpbroker allows you to telnet out from behind a firewall to another system also behind a firewall via a proxy host running the broker.

The regular version does SRP authentication, and so needs a special client, brokerclient. brokerclient just connects to the remote port and begins the client side authentication. After that it just passes data through. The default username is "broker" and the passphrase is "nakaniau" (Japanese for "meet in the middle"). The passphrase can be set with tphrase from the libtinysrp distribution system.

The tinysrp protocol currently doesnt do synchronization, so the brokers authentication code is slightly more complicated than one function call... But the broker needs to do synchronization anyway to determine which end of the connection to authenticate. Client synchronization is necessary when going through a proxy, where there is a preamble of commands to the proxy/gateway server, and the proxy can return arbitrary junk. Currently, the preamble is hardcoded (off by default); see the comments in brokerclient.c.

DaemonRip runs as a Unix daemon and polls a CD drive to see if an audio CD is inserted.

When an audio CD is detected, it will automatically connect to a CDDB server to determine the name, artists, and tracks of the CD, and begin to rip and encode the CD using your preferred ripping and encoding applications.

When finished ripping the disc, it will be ejected from the drive, allowing you to insert a new one to continue the process. No other user interaction is required.

DaemonRip project also can keep statistics about your ripping and encoding times, and logs all of the actions to a log file.

httptype is a program that returns the http host software of a website. It is written in Perl.
httptype reads a list of http hosts and optionally the port number for each of these. It queries each host, displaying the type of HTTP server running on that host. It reads the http_proxy and no_proxy environment variables to determine whether to use a proxy or not.
httptype reads a list of http servers and, optionally, the port number for each of these. It then queries each of the hosts and displays the HTTP server software of the host.
Input may be read from a host file if specified using the --hosts switch:
httptype --hosts [hostfile]
If hostfile is omitted or `-, httptype reads from standard input. See Format of host file for more info.
A single host may be queried by passing its name on the command line:
httptype host [port]
If port is omitted, 80 is used.
If no host file is specified through the --hosts file and no host is specified on the command line, httptype will read the list from standard input. See Format of host file for more info.
httptype will read the http_proxy environment variable and try to determine if a proxy server is being used. This setting may be overridden using the --proxy switch:
httptype --proxy proxyhost[:proxyport]
If proxyport is omitted, 80 is used.
If the proxy server is `none, no proxy is used. This is typically used to prevent httptype from using the proxy server specified by http_proxy. The --noproxy switch can be used to achieve the same.
Additionally, you may use the no_proxy environment variable to specify a comma delimited list of hosts for which httptype should not use the proxy. If httptype comes across any of these hosts, it will make a direct connection to them.
Enhancements:
- made 1.3.8 stable and renamed to 1.2.3

Bio::SAGE::DataProcessing module processes raw serial analysis of gene expression (SAGE) data.

SYNOPSIS

use Bio::SAGE::DataProcessing;
$sage = Bio::SAGE::DataProcessing->new();

# open sequence and quality files
open( READS, "library.fasta" );
open( QUAL, "library.qual.fasta" );

# collect ditags and statistics from reads
$sage->process_library( *READS, *QUAL );

# close files
close( READS );
close( QUAL );

# output tags in descending order of expression
my %tags = %{$sage->get_tagcounts()};
open( TAGS, ">library.tags" );
map { print TAGS join( "t", $_, $tags{$_} ) . "n" } sort { $tags{$b} $tags{$a} } keys %tags;
close( TAGS );

# tag AAACCGGGTT matches two different genes
# so 15th base pair may help resolve this
$sage->print_extra_base_calculation( $sage->get_extract_base_calculation( "AAACCGGGTT" ) );

This module provides several tools for processing and analyzing serial analysis of gene expression (SAGE) libraries.

Serial analysis of gene expression (SAGE) is a molecular technique for generating a near-global snapshot of a cell population’s transcriptome. Briefly, the technique extracts short sequences at defined positions of transcribed mRNA. These short sequences are then paired to form ditags. The ditags are concatamerized to form long sequences that are then cloned. The cloned DNA is then sequenced. Bioinformatic techniques are then employed to determine the original short tag sequences, and to derive their progenitor mRNA. The number of times a particular tag is observed can be used to quantitate the amount of a particular transcript. The original technique was described by Velculescu et al. (1995) and utilized an ~14bp sequence tag. A modified protocol was introduced by Saha et al. (2002) that produced ~21bp tags.

PURPOSE

This module facilitates the processing of SAGE data. Specifically:

1. extracting ditags from raw sequence reads.
2. extracting tags from ditags, with the option to
exclude tags if the Phred scores (described by
Ewing and Green, 1998a and Ewing et al., 1998b)
do not meet a minimum cutoff value.
3. calculating descriptive values
4. statistical analysis to determine, where possible,
additional nucleotides to extend the length of the
SAGE tag (thus facilitating more accurate tag to
gene mapping).

Both regular SAGE (14mer tag) and LongSAGE (21mer tag) are supported by this module. Future protocols should be configurable with this module.