<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36216?offset=100 https://bioinformaticsonline.com/pages/view/33840/awesome-perl-frameworks-libraries-and-software-part-3 Fri, 07 Jul 2017 04:10:32 -0500 https://bioinformaticsonline.com/pages/view/33840/awesome-perl-frameworks-libraries-and-software-part-3 <![CDATA[Awesome perl frameworks, libraries and software - PART 3]]>
  • fujiwara/perl-queue-q4pg-lite - simple message queue using PostgreSQL.
  • formbuilder/formbuilder - Perl CGI::FormBuilder module for generating, validating, and processing HTML forms
  • fastly/fastly-perl - Fastly perl client
  • ewilded/SCARY - PHP Source Code Analyzer written in Perl (taint checking)
  • esobchenko/rest-google - REST::Google provides OO access to Google REST API from Perl
  • Ensembl/Bio-DB-HTS - Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib
  • eblah/E-Blah-Forum - E-Blah is a Perl-based forum system started in 2001.
  • dominikschulz/Zabbix-Sender - A pure-perl implementation of zabbix-sender.
  • derf/Travel-Status-DE-IRIS - IRIS Perl API (German and partially european railway departure monitor)
  • Debian/devscripts - Mirror of https://anonscm.debian.org/cgit/collab-maint/devscripts.git
  • ddmitov/camel-doctor - Desktop HTML User Interface for the default Perl 5 Debugger :dromedary_camel:
  • dan-blanchard/io-storm - :zap: Perl support for Apache Storm distributed computation system.
  • dajobe/logger - Perl IRC logger
  • dagolden/Hash-Ordered - A compact, pure-Perl ordered hash class
  • dagolden/getopt-lucid - (Perl) Clear, readable syntax for command line processing
  • craigslist/perl-AnyEvent-Redis-Federated - An event-based redis client that implements client-side sharding in Perl.
  • cosimo/perl5-device-modem - Device::Modem CPAN module, interface to any AT-command-set based device
  • CindyLinz/Perl-AnyEvent-MySQL - Pure Perl AnyEvent socket implementation of MySQL client
  • chorny/test-warn - Perl extension to test methods for warnings
  • cho45/List-Enumerator - List::Enumerator is like ruby's Enumerator. (Perl)
  • bingos/module-install-readmefrompod - (perl) A Module::Install extension to automatically convert POD to a README
  • bingos/bot-gumbynet - (perl) The GumbyNET bot code
  • aufflick/p5-net-apns-persistent - Persistent Apple APNS interface for Perl 5
  • ddmitov/perl-executing-browser - HTML User Interface for Perl 5 Desktop Applications :dromedary_camel:
  • phatblat/app-store-rank - A simple Perl script which scrapes the 62 app stores worldwide for the current app ranking
  • Easy-Forex/Verify-emails - Quick perl script to check a list of email addresses for valid and bogus.
  • warewolf/Procmon - A perl command toolkit for analysis of XML procmon logs
  • typester/data-amf - perl module for serialize/deserialize adobe's AMF data
  • thibaultduponchelle/tryperl - Try Perl: learn the basics of the Perl language in your browser
  • syohex/new-tohoho - Modernize 「とほほの perl入門」
  • simcop2387/perlbuut - new version of perlbot, based on buubot
  • rjray/image-size - A Perl module to read the dimensions of images in several popular formats
  • perigrin/flexo-bot - A Rewrite of the Bender IRC bot from irc.perl.org using the Adam/Moses framework
  • norm/p5-Media - Perl modules and scripts for handling the conversion and storage of media
  • nkakuev/list-cpp-warning-options - A simple Perl script that prints GCC warning options you can apply to C++ code.
  • mscoutermarsh/RRD-to-CSV - Perl script to convert RRD data to CSV
  • mones/clawsker - This is a clone from main repository at http://git.claws-mail.org: Clawsker is a Perl-GTK2 applet to edit hidden preferences for Claws Mail, and to do it in a safe and user friendly way, preventing users from raw editing of configuration files.
  • mackers/passook - Passook is a perl script that automatically generates passwords. Passook is customizable so that you can choose different levels between a very pronounceable or a very secure password. Passook can be run in a unix shell or as a cgi script.
  • lecstor/PDF--Boxer - Perl module to create PDF documents from "simple" templates.
  • jmcnamara/app-pod2epub - A Perl Module for converting Pod to ePub eBooks.
  • jjn1056/Example-PlackStreamingAndNonblocking - Examples of Perl Plack / PSGI streaming and nonblocking
  • hoytech/Valence-p5 - Perl interface to valence/electron GUI toolkit
  • erinspice/geni-automerge - A tool written in Perl using the Geni.com API which automatically merges sufficiently similar profiles.
  • eilara/camel-defense - A very simple tower defense game in Perl
  • clintongormley/ElasticSearchX-Autocomplete - ElasticSearchX::Autocomplete is a Perl module which gives you frequency (and optionally geolocation)-sensitive autocomplete suggestions based on your data
  • audreyt/encode-hanconvert - [Perl] Modules and scripts for Traditional and Simplified Chinese mappings
  • szabgab/perltv.org - The source code of the Perl TV
  • rhandom/perl-net-server - Perl Module Net::Server
  • plotly/Perl-API - Perl-API for beautiful, interactive, & shareable graphs
  • MerijntjeTak/vyattaLookingGlass - Looking glass for the Vyatta routing suite
  • KES777/Devel-DebugHooks - Perl debugger
  • jonasbn/perl-workflow - Simple, flexible system to implement workflows
  • inway/mojo-rabbitmq-client - Mojo::IOLoop based RabbitMQ (AMQP) client
  • ingydotnet/yaml-pm - YAML Perl Module
  • gtsafas/mailgun.perl - Perl wrapper for mailgun
  • abaez/perl - Learning Perl
  • technix/Perl-Analyzer - Perl source analyzer - view namespaces, dependencies, inheritance and much more
  • zigorou/perl-json-patch - A Perl implementation of JSON Patch
  • Yaribz/SPADS - SpringRTS Perl Autohost for Dedicated Server
  • vti/app-prf - Perl refactoring tool
  • TvdW/perl-DBD-Cassandra - DBD::Cassandra is a DBI driver for Cassandra/CQL3
  • topaz/perl-mandelbrot - Interactive Mandelbrot set renderer/explorer for your terminal.
  • tociyuki/libtext-ampita-perl - Template generator from a xhtml document and runtime for it.
  • tene/perl6-sqlite - SQLite3 for Perl 6
  • smarx/waz-storage-perl - Small library for working with Windows Azure storage from Perl
  • scottchiefbaker/perl-git-prompt - Git extension for the bash prompt
  • sbober/levitation-perl - perl port of scy's levitation
  • salva/p5-Net-SFTP-Foreign - Perl SFTP client
  • russoz/perltests - Small scripts to test constructs - mostly for myself.
  • robrwo/Perl-Rewrite - Munge Perl Code
  • rjbs/IPC-Run3 - (Perl) run a subprocess with input/ouput redirection
  • rjbs/Email-Simple - the Email-Simple perl distribution
  • ritou/p5-oidc-lite - OIDC::Lite - Perl Library of OpenID Connect
  • pjf/WebService-HabitRPG - Access the HabitRPG API from Perl
  • pjf/trillr - Perl tip example code
  • PerlBone/PerlBone - PerlBone allows you to write Arduino Style software in Perl for the BeagleBone. It is to Perl what BoneScript is to Javascript
  • Ovid/code-cutnpaste - Find cut-n-pasted Perl code
  • mfontani/Net-Amazon-Route53 - Perl interface to Amazon's Route 53 service
  • maxmind/GeoIP2-perl - Perl API for MaxMind's GeoIP2 web services and databases
  • maros/CatalystX-I18N - Perl I18N Toolkit for the Catalyst MVC
  • marcusramberg/text-simpletable - The Text::SimpleTable perl distribution
  • lovelle/perl-disque - Perl client for Disque, an in-memory, distributed job queue
  • leto/math--matrixreal - Matrices of real numbers in Perl
  • Klortho/Physics-Unit - Perl Physics::Unit module
  • kentaro/perl-project-libs - Include modules libs automatically
  • karpet/search-query-perl - Search::Query - polyglot query parsing
  • jplindstrom/p5-Devel-PerlySense - CPAN module Devel::PerlySense
  • hvoers/PNL - Site for Perl mongers in NL
  • HouzuoGuo/PerlDB - This is a programming exercise, do not use in serious code.
  • hirose31/p5-InfluxDB - Perl client library for InfluxDB
  • grantm/XML-SAX - Simple API for XML including pure Perl parser
  • GeneticGenesis/Perl-Ferment - Yet another tool to manage perl installs in your home directory.
  • Ensembl/ensembl-funcgen - Ensembl Funcgen Perl API and SQL schema
  • dk/Win32-GuiTest - Perl GUI Test Utilities
  • depesz/Pg--Explain - Pg::Explain Perl module
  • dann/p5-perl-metrics-lite - Pluggable Perl Metrics System
  • daisieh/phylogenomics - (Mostly) Perl scripts that do something related to phylogenomic analysis.
  • carwynmoore/perl-nats - A Perl client for the NATS messaging system
  • briandfoy/test-prereq - (Perl) check if Makefile.PL has the right pre-requisites
  • briandfoy/cpan-packagedetails - (Perl) This is what the module does
  • bingos/cpanplus-yacsmoke - (perl) Yet Another CPANPLUS Smoke Tester
  • beanz/net-mqtt-perl - Perl implementation of MQTT Protocol (http://mqtt.org)
  • perl6/book - Using Perl 6 - an unfinished book about Perl 6
  • lukec/stripe-perl - Perl library to connect to the Stripe API
  • c0bra/image-wordcloud-perl - Perl module for generating pretty wordcloud images
  • bradfitz/set-consistenthash-perl - consistent hashing library for Perl
  • wolfman2000/Perl-6-Pastebin - A pastebin written in Perl 5 to host content specifically meant for Perl 6.
  • njh/perl-net-rtp - Perl Module : Send and receive RTP packets (RFC3550)
  • beanz/net-pachube-perl - Perl Interface to Pachube
  • apparentlymart/perl-anyevent-websocket - WebSocket implementation for AnyEvent
  • tsee/ZMQ-Declare-Perl - The ZMQ::Declare Perl module for declarative use of 0MQ
  • sjohnston/Net-Zabbix - Perl wrapper for Zabbix API
  • reneeb/Perl-Critic-OTRS - A collection of Perl::Critic policies to program in the OTRS way.
  • masak/csv - A parser for CSV (comma-separated values) files for Perl 6
  • jtbraun/Parse-RecDescent - Perl module for generating recursive-descent parsers
  • jjn1056/perl-recruiting-web - webpages for helping recruiters and perl programmers understand each other better
  • chef-boneyard/chef-install - A perl based installer for Chef
  • pvande/Template-Mustache - Drawing Mustaches on Perl, for fun and profit
  • schwern/Paths - Grand Unified Perl File and Directory Objects
  • schwern/Gravatar-URL - Perl module to make URLs for Gravatars from an email address
  • p5-shorten/WWW-Shorten-Yourls - Perl module for shortening URLs using yourls.org
  • juliensobrier/Net-Google-SafeBrowsing2 - Google Safe Browsing v2 library for Perl
  • EntropyOrg/p5-Devel-IPerl - :microscope::books: Perl language kernel for Jupyter http://jupyter.org/
  • PerlChina/HeadFirstMoose - 使用Perl + Moose实现《Head First Design Pattern》的大部分例子
  • mudler/GitInsight - Predict your github contributions using Bayesian inference and Markov chain with perl and PDL
  • dagolden/File-chdir - (Perl) a more sensible way to change directories
  • potyl/perl-App-deckjs2pdf - Convert a Deck.JS presentation to PDF
  • Perl-Toolchain-Gang/Sub-Uplevel - (Perl) apparently run a function in a higher stack frame
  • mlawren/p5-OptArgs - Integrated option and argument processing for Perl scripts
  • masterzen/redis-snmp - A perl net-snmp agentX to export Redis performance counters
  • masochist/modern-perl-cpan-task-kensho - The repository for the upcoming book, Modern Perl with CPAN
  • jeffa/DesignPatterns-Perl - Perl (with Moose) implementations of the Gang of Four Design Patterns
  • agentzh/makefile-parser-pm - Perl CPAN module Makefile::Parser - A simple parser for Makefiles
  • Real-Gecko/filemin - File manager for Webmin written completely in perl
  • andreas-marschke/nagios-nrpe - A pure perl implementation of the Nagios NRPE daemon and client
  • syohex/zsh-perl-completions - zsh completions for Perl utilties
  • pclinger/SonyCameraRemote - Sony Camera Remote API - Perl Implementation
  • patch/cldr-number-pm5 - CLDR::Number (Perl 5): Localized number formatters using the Unicode CLDR
  • ollyg/Net-CLI-Interact - Development of Net::CLI::Interact Perl distribution
  • nothingmuch/continuation-delimited - delimited continuations for Perl 5
  • nmelnick/whatbot - whatbot: A sane bot for most chat applications, written in modern Perl
  • naoya/list-rubylike - Ruby-like list operations for perl
  • miyagawa/CPAN-Any - Install Perl modules using any CPAN clients
  • miki/Algorithm-LSH - perl implementation of Locality Sensitive Hashing
  • kimmel/basic-perl-template-for-cli - A basic template for Perl applications that take and parse command line options. Based on the ideas from Perl Best Practices and the GNU style long options reference. It uses only Standard Modules to maintain portability.
  • gardejo/moose-presentations - Perl Moose course in Japanese
  • dpavlin/Biblio-RFID - perl tools to use different RFID readers for library use
  • chef/chef-install - A perl based installer for Chef
  • bingos/smokebrew - (perl) Automated Perl building and installation for CPAN Testers
  • andrewrjones/perl5-App-MP4Meta - Apply iTunes-like meta data to an mp4 file
  • admc/irssi-growlnotify - Creating Growl notifications from various Irssi events, using growlnotify and Irssi Perl.
  • plack/psgi-specs - PSGI (Perl WSGI) specifications
  • libwww-perl/uri - The Perl URI:: module
  • autarch/DateTime.pm - A date and time object for Perl
  • zostay/P6SGI - Proposed Standard for Perl 6 Web Server Gateway Interface Specification
  • cooper/yiria - the current generation of juno-ircd, an IRC server daemon written in the Perl programming language. it's very modular and event-driven, designed specifically to be extensible and aims to implement all modern features of IRC, including those of many recently-defined specifications.
  • wertarbyte/hetzner-rdns - update reverse DNS settings for systems hosted at Hetzner; a successor (hetzner-robot-perl) is in preparation to utilise the webservice interface
  • spencertipping/canard - A functional concatenative language implemented in Linux/AMD64 machine code and self-modifying perl
  • sni/Monitoring-Generator-TestConfig - Perl extension for generating test monitoring configurations (nagios/icinga/shinken)
  • slazar/Panasonic-LF20-control - Perl Scripts to control the Panasonic LF20 LCD TV Series
  • sabujp/nfsSpeedTest - nfsSpeedTest is a wrapper for dd written in Perl. It was created mainly for testing the performance of file systems or network file shares (e.g. NFS), but can be used for generating large files (e.g. swap files) or for testing the network
  • quietfanatic/link-c - Easily use C libraries in Rakudo Perl 6
  • pjain/WWW-Shorten-Yourls - Perl module for shortening URLs using yourls.org
  • nightsailer/net-sinaweibo - A lightweight Perl OAuth api for SinaWeibo(新浪微博)
  • mbethke/Ashafix - A Postfixadmin clone in Perl/Mojolicious
  • kzys/test-mock-recorder - Record-and-verify style mocking library for Perl
  • kpumuk/mysqlsla-bdb - MySQL Slow Logs Analyzer optimized to work with huge logs (use BerkeleyDB instead of perl hashes)
  • hernan604/Web-IRC - The purpose of Web::IRC is to help team communication. Web::IRC uses channel concept from IRC. Slack.com clone in perl <3
  • duckduckgo/p5-duckpan-installer - DuckPAN Perl Installer
  • dnmfarrell/Perly-Bot - a RSS trawler and social media broadcaster
  • PDLPorters/PDL-Stats - Statistics modules in Perl Data Language, with a quick-start guide for non-PDL people. They make the PDL shell work like R, but with PDL threading (fast automatic iteration) of procedures including t-test, linear regression, and k-means clustering.
  • CPAN-API/metacpan-client - Home of the official MetaCPAN Perl API client.
  • rrb3942/perl-Asterisk-AMI - A Perl module for interfacing with the Asterisk Management Interface.
  • rafl/perlfaq - History of the perlfaq distribution before it got moved to https://github.com/tpf/perlfaq
  • mithun/perl-tmdb - TMDB - Perl wrapper for The MovieDB API
  • hyphaltip/htbda_perl_class - High Throughput Biological Data Analysis using Perl
  • gmcharlt/marc-perl - MARC/Perl (mirror of git://git.code.sf.net/p/marcpm/code)
  • cosimo/perl5-http-dav - Perl5 HTTP::DAV CPAN module, interface to WebDAV-enabled HTTP servers
  • copperly/Perl-Tutorial - Tutorial for Perl
  • apocalypse/perl-dist-zilla-plugin-authority - add an $AUTHORITY to your packages
  • DrHyde/perlscripts - Random scripts
  • perl6/DBIish - Database interface for Perl 6
  • shlomif/mastering-perl - A copy of brian d foy's mastering-perl book.
  • Prajithp/letsencrypt-cpanel - cPanel/WHM plugin for Let's Encrypt client (uses perl and WHM API)
  • mikecardwell/pipe2imap - Pipe2IMAP is a Perl script that will take IMAP options from the command line arguments, and an email from a PIPE, and will deliver the message via IMAP
  • silverstripe-labs/silverstripe-unidecode - Unidecode is a PHP version of the perl module Text::Unicode. It takes UTF-8 data and tries to represent it in US-ASCII characters.
  • exhuma/jsttyplay - A set of scripts written in Perl and JavaScript to allow ttyrec logs to be played back in a web browser.
  • demianriccardi/HackaMol - Object-Oriented Perl 5, Moose Library for Molecular Hacking
  • davorg/www-shorten - Perl interface to various URL-shortening sites
  • agentzh/queue-memcached-buffered - Perl client library for memcacheq operations
  • toronto-perl-mongers/tpm-website - Toronto Perl Mongers Website
  • odyniec/p5-WebService-Amazon-Route53 - Perl interface to Amazon Route 53 API
  • neilb/perl-hub - Proof of concept for "front page for the perl community"
  • mschilli/proc-simple-perl - Proc::Simple CPAN Module
  • makamaka/geohex-perl - geohex perl implementation (Geo::Hex)
  • gslin/thrift-perl - Perl module of Thrift
  • djzort/Net-DHCP - Perl module Net::DHCP
  • cosimo/perl5-test-device-serialport - A mock object to test virtual serial port-based devices
  • afair/resque-perl - Resque ported to perl
  • PerlChina/Newbie-Gift - A tool suite for perl newbie.
  • Perl-Email-Project/Email-Send - perl library for sending email
  • Lemonade-Stand/Lemonade - Perl E-commerce Solution
  • atomicules/TTYtter - Unofficial maintenance and mirror of Floodgap's TTYtter: an interactive console text-based command-line Twitter client and Perl platform (whew!)
  • worldmind/perl-test-code-quality-template - Some tests for non-functional testing - you can copy these test to any your perl project
  • dpavlin/perl-fuse - write filesystems in Perl using FUSE
  • rjbs/Email-Valid - perl library to validate email addresses
  • masak/gge - Glacial Grammar Engine -- a Perl 6 grammar engine written in Perl 6
  • masak/druid - A connection-oriented board game written in Perl 6
  • harisekhon/lib - Perl & Python Utility Library for my other repos
  • tempire/riak-tiny - Perl interface to Riak without Moose
  • oz/tiny_wiki - 50 lines of Perl to play around with Dancer and KiokuDB
  • goozbach/perl-Net-Disqus - A Perl library for the Disqus API -- Deprecated
  • borisdaeppen/VM-JiffyBox - Perl API for JiffyBox
  • apeiron/modern-perl-cpan-task-kensho - The repository for the upcoming book, Modern Perl with CPAN
  • ajolma/geoinformatica - Geoinformatica is a geospatial toolkit that builds on GDAL, Perl and GTK+
  • Weborama/Riak-Light - Fast and lightweight Perl client for Riak
  • zostay/owasp-esapi-perl - OWASP Enterprise Security API for Perl
  • yannk/perl-net-appnotifications - perl5 interface to www.appnotifications.com: easily deliver push notifications to your iPhone
  • three18ti/Reddit.pm - Perl wrapper for the reddit API
  • sukria/Test-TinyMocker - Minimal yet very useful mocker for Perl
  • solgenomics/yapri - Yet Another Perl R Inteface.
  • rclasen/workout - Workout file perl library
  • pshangov/perldoc-vim - Perldoc viewer for vim with syntax highlighting
  • olof/transmission-client - Perl interface to Transmission bittorrent client
  • ogawa/cybozu2ical-perl - Converting Cybozu Office Scheduler data to iCalendar format.
  • motemen/perl5-Print-Indented - Outputs indented as per source code indentation
  • miknight/pisg - Perl IRC Statistics Generator
  • melo/bash-completion - A Perl distribution to create your own bash completion solutions
  • mantovani/SPPM-Web - São Paulo Perl Mongers website.
  • jzawodn/perl-Algorithm-TopPercent - A perl module for tracking the top-N most frequent items in a streaming data set using fixed memory.
  • jmlynesjr/wxPerl-Module-Examples - wxPerl-Module-Examples not from the wxBook
  • doy/parse-keyword - DEPRECATED: write syntax extensions in perl
  • chromatic/Test-MockObject - The Test::MockObject Perl 5 library from the CPAN
  • chrisa/perl-Net-ZooKeeper - Net::ZooKeeper Perl module
  • apparentlymart/activity-streams-perl - Activity Streams Library for Perl
  • andrewalker/p5-webservice-digitalocean - Perl module for DigitalOcean's RESTful API
  • Starlink/perl-Astro-FITS-HdrTrans - Perl module for performing astronomical metadata header translations from FITS to generic and back.
  • Rio-Perl-Mongers/rio.pm.org - Site da Rio Perl Mongers
  • sitaramc/gitolite - Hosting git repositories -- Gitolite allows you to setup git hosting on a central server, with very fine-grained access control and many (many!) more powerful features. [IMPORTANT: please click and read the WIKI link above before submitting issues, pull requests, etc] IMPORTANT: PLEASE READ Nov 2 2014 UPDATE ABOUT DONATIONS -- see wiki
  • openresty/lua-nginx-module - Embed the Power of Lua into NGINX
  • sarabander/sicp-pdf - SICP PDF with Texinfo and LaTeX source
  • openresty/ngx_openresty - Turning Nginx into a Full-fledged Web App Server
  • petdance/ack - This repository is for ack 1.x, which is no longer being maintained. DO NOT SUBMIT ISSUES HERE. ack 2.0 has a new GitHub project at
  • openresty/nginx-tutorials - Nginx Tutorials
  • creaktive/rainbarf - CPU/RAM/battery stats chart bar for tmux (and GNU screen)
  • thoughtbot/rcm - rc file (dotfile) management
  • prey/prey-bash-client - Bash client for the Prey anti-theft software (Mac, Windows, Linux). The original.
  • lulzlabs/AirChat - Free Communications For Everyone.
  • k4rthik/git-cal - github like contributions calendar on terminal
  • munin-monitoring/contrib - Contributed stuff for munin (plugins, tools, etc...)
  • duckduckgo/duckduckgo - DuckDuckGo Instant Answer Infrastructure
  • nbs-system/naxsi - NAXSI is an open-source, high performance, low rules maintenance WAF for NGINX
  • DHowett/theos - Unified cross-platform iPhone Makefile system
  • git-deploy/git-deploy - Tool to manage using git as a deployment management tool
  • munin-monitoring/munin - Main repository for munin master / node / plugins
  • theory/sqitch - Sane database change management
  • jonreid/XcodeCoverage - Code coverage for Xcode projects
  • dalibo/pgbadger - a fast PostgreSQL Log Analyzer
  • nferraz/st - simple statistics from the command line
  • yuki-kimoto/gitprep - Github clone. you can install Github system into your unix/linux machine.
  • miyagawa/cpanminus - cpanminus - get, unpack, build and install modules from CPAN
  • sullo/nikto - Nikto web server scanner
  • sontek/dotfiles - My configuration files (.screenrc, .vimrc, .weechat, .bashrc, .gitconfig, etc)
  • PenturaLabs/Linux_Exploit_Suggester - Linux Exploit Suggester; based on operating system release number
  • RexOps/Rex - A framework for server orchestration and to simplify system administration
  • hokaccha/nodebrew - Node.js version manager
  • pasky/speedread - A simple terminal-based open source Spritz-alike (per-word RSVP aligned on optimal reading points)
  • plack/Plack - PSGI toolkit and server adapters
  • get-iplayer/get_iplayer - A utility for downloading TV and radio from BBC iPlayer
  • jfhovinne/jFeed - jQuery RSS/ATOM feed parser plugin
  • openresty/lua-resty-redis - Lua redis client driver for the ngx_lua based on the cosocket API
  • StefanSchroeder/Golang-Regex-Tutorial - Golang - Regular Expression Tutorial
  • openresty/nginx-systemtap-toolkit - Real-time analyzing and diagnosing tools for Nginx based on SystemTap
  • webfrogs/xcode_shell - shell script that used to auto-build xcode project
  • linode/cli - Command-line interface to the Linode platform
  • agentzh/code2ebook - Generate ebooks in various formats from source trees in various programming languages
  • timkay/aws - Easy command line access to Amazon EC2, S3, SQS, ELB, and SDB (new!)
  • webmin/webmin - Webmin source code
  • freebsdgirl/ggautoblocker - Good Game Auto Blocker
  • openresty/headers-more-nginx-module - Set, add, and clear arbitrary output headers
  • swcarpentry/bc - This repository is now frozen - please see the note below.
  • sm/sm - S{cripting,ystem,tack} Management (SM) Framework (Core)
  • alestic/ec2-consistent-snapshot - Initiate consistent EBS snapshots in Amazon EC2
  • bestpractical/rt - Request Tracker, an enterprise-grade issue tracking system
  • trapd00r/ls-- - ls on steroids
  • movabletype/movabletype - Movable Type
  • gotgit/gotgit - Errata and resources for GotGit: a book about Git in Chinese
  • ljunkie/plexWatch - Notify and Log watched content on a Plex Media Server
  • joeyh/myrepos - Multiple Repository management tool
  • xypiie/spread0r - spread0r is a txt reader, which makes your reading twice as fast as usual
  • linode/longview - Linode Longview Agent
  • philovivero/distribution - Short, simple, direct scripts for creating ASCII graphical histograms in the terminal.
  • mysociety/fixmystreet - This is mySociety's popular map-based reporting platform: easy to install in new countries and regions
  • spencertipping/js-in-ten-minutes - JavaScript in Ten (arbitrarily long) Minutes
  • kazeburo/GrowthForecast - Lightning Fast Graphing/Visualization
  • qooob/authentic-theme - Webmin/Usermin/Virtualmin/Cloudmin theme based on Bootstrap and Font Awesome
  • jbittel/httpry - HTTP logging and information retrieval tool
  • zakk4223/CocoaSplit - Stream/record your desktop/webcam to twitch/owned etc.
  • miyagawa/github-growler - Growl github updates
  • VividCortex/johnny-deps - Barebones dependency manager for Go.
  • dotphiles/dotphiles - A community driven framework of dotfiles.
  • CPAN-API/metacpan-web - Web interface for MetaCPAN
  • worlduniting/bookshop - bookShop is a publishing framework for html-to-pdf/(e)book toolchain happiness and sustainable productivity.
  • duncs/clusterssh - Cluster SSH - Cluster Admin Via SSH
  • leedo/noembed - oEmbed gateway service with additional non-oEmbed sources
  • cxreg/smartcd - Alter your bash (or zsh) environment as you cd
  • perl-catalyst/catalyst-runtime - The Elegant MVC Web Application Framework
  • Flipkart/HostDB - HostDB: a new tool to help manage data center inventory and write applications around it.
  • metabrainz/musicbrainz-server - The official musicbrainz-server codebase
  • monsieurvideo/get-flash-videos - Download or play videos from various Flash-based video hosting sites, without having to use the Flash player.
  • c9s/Vimana - Vimana is an easy to use system for searching , installing, and downloading vim script. Vimana provides a command-line interface such like aptitude programe on Debian linux, for you to search , download , install , upgrade scripts from http://www.vim.org (vimonline site).
  • Logitech/slimserver - Server for Logitech Squeezebox players. This server is also called Logitech Media Server
  • weijianwen/SJTUThesis - XeLaTeX templates for Shanghai Jiao Tong University (SJTU) thesis
  • hadley/ggplot2-book - The ggplot2 book
  • irssi/scripts.irssi.org - Script Repository for Irssi
  • bucardo/check_postgres - Nagios check_postgres plugin for checking status of PostgreSQL databases
  • harisekhon/nagios-plugins - Advanced Nagios Plugins - Hadoop, NoSQL datastores. Extends Nagios monitoring capabilities significantly further in to the application layer including Hadoop, Big Data, NoSQL and Web Scale technologies, APIs etc.
  • benbernard/RecordStream - commandline tools for slicing and dicing JSON records.
  • iberianpig/xSwipe - Multitouch gestures on X11, Linux
  • jimeh/manservant - Browse man pages in style with your personal manservant.
  • joeyh/ikiwiki - a wiki compiler
  • Zentyal/zentyal - Linux Small Business Server
  • yaoweibin/nginx_ajp_module - support AJP protocol proxy with Nginx
  • CPAN-API/cpan-api - A free, open API for everything you want to know about CPAN
  • neldredge/mathgen - See http://thatsmathematics.com/mathgen/
  • jtaby/Waldo - A generic port of TextMate's Find-In-Project, with associated MacVim plugin
  • broquaint/Gitalist - A modern git web viewer
  • rtomayko/shocco - shocco is a quick-and-dirty, literate-programming-style documentation generator for / in POSIX shell
  • pjf/exobrain - Automate your life with Exobrain
  • miyagawa/plagger - Pluggable RSS/Atom aggregator
  • justone/dotfiles - Dotfiles
  • jsierles/chef_cookbooks_deprecated - Opinionated chef recipes for Ubuntu/Debian. Manage nginx, unicorn, UNIX user accounts, postgresql, and more!
  • mattiasgeniar/varnish-4.0-configuration-templates - Configuration templates used for Varnish 4.0 implementations.
  • openresty/lua-resty-mysql - Nonblocking Lua MySQL driver library for ngx_lua
  • proger/eflame - Flame Graph profiler for Erlang
  • openresty/stapxx - Simple macro language extentions to systemtap
  • dkogan/feedgnuplot - Tool to plot realtime and stored data from the commandline, using gnuplot. This is the repo for 'feedgnuplot' on CPAN
  • wbraswell/rperl - RPerl Compiler
  • petdance/bobby-tables - bobby-tables.com, the site for preventing SQL injections
  • pshved/timeout - A script to measure and limit CPU time and memory consumption of black-box processes in Linux
  • openresty/srcache-nginx-module - Transparent subrequest-based caching layout for arbitrary nginx locations.
  • dockerana/dockerana - Docker Monitoring with support for Grafana and Graphite
  • OTRS/otrs - The OTRS framework.
  • bucardo/bucardo - Bucardo multimaster and master/slave Postgres replication
  • rjbs/Dist-Zilla - scary tools for building CPAN distributions
  • kjellm/munin-mysql - Improved MySQL Graphs for Munin
  • holygeek/git-number - Use numbers for dealing with files in git
  • s-aska/dropbox-api-command - Dropbox API wrapper command.
  • pintsized/ledge - A Lua application for OpenResty, providing scriptable HTTP cache functionality for Nginx.
  • rcarmo/textwrangler-bbedit-solarized - solarized color scheme for BBEdit and TextWrangler
  • lamw/vghetto-scripts - Various virtuallyGhetto scripts for VMware based solutions
  • tokuhirom/Amon - yet another web application framework
  • cschneid/irclogger - Sinatra based irclogger.com
  • andrewning/sortphotos - SortPhotos is a Python script that organizes photos and videos into folders using date/time information
  • pintsized/lua-resty-http - Lua HTTP client cosocket driver for OpenResty / ngx_lua.
  • jamesc/nagios-plugins-rabbitmq - A set of nagios checks for RabbitMQ using the management interface
  • kazeburo/cloudforecast - the server metrics gathering
  • zigdon/twirssi - An irssi script allowing the use of Twitter from within the IRC client.
  • ganglia/gmetric - Repository of user-contributed gmetric scripts
  • joemiller/collectd-graphite - collectd plugin for sending data to graphite
  • naoya/md2inao - Convert markdown to inao-format for WEB+DB PRESS
  • inverse-inc/packetfence - PacketFence is a fully supported, trusted, Free and Open Source network access control (NAC) solution. Boasting an impressive feature set including a captive-portal for registration and remediation, centralized wired and wireless management, powerful guest management options, 802.1X support, layer-2 isolation of problematic devices; PacketFence can be used to effectively secure networks small to very large heterogeneous networks.
  • devd/Academic-Writing-Check - check for passive words, weasel words, duplicate words, typographical errors and words strunk & white don't like
  • yoshinorim/mha4mysql-manager - Development tree of Master High Availability Manager and tools for MySQL (MHA), Manager part
  • yaoweibin/ngx_http_substitutions_filter_module - a filter module which can do both regular expression and fixed string substitutions for nginx
  • yaoweibin/nginx_syslog_patch - add the full syslog feature to Nginx
  • jjl/get_iplayer - A utility for grabbing tv and radio from BBC iPlayer. Phil Lewis has stopped developed it so I've forked it.
  • kost/dvcs-ripper - Rip web accessible (distributed) version control systems: SVN/GIT/HG...
  • mrash/fwknop - Single Packet Authorization > Port Knocking
  • majutsushi/urxvt-font-size - Change the urxvt font size on the fly
  • apenwarr/gitbuilder - Auto-builds and tests all the branches of your git projects, showing pass/fail results on a web page/RSS feed. Isolates failures to the first commit that caused the problem.
  • tangledhelix/dotfiles - My dotfiles
  • shabble/irssi-scripts - Repo to store some personal irssi scripts
  • kud/jpegrescan - JPEGrescan: losslessly shrink any JPEG file.
  • gregkh/bti - bash twitter ididocy
  • woothee/woothee - User-Agent parser/classifier for multi languages
  • spencertipping/nfu - Numeric Fu for the command line
  • davidbauer/Instacurate - Turn your Twitter timeline into a personalised news site, in an instant. Fetches links from your timeline and displays them in a discovery friendly design.
  • yuri-gushin/Roboo - Roboo - HTTP Robot Mitigator
  • kni/redis-sharding - Redis Sharding is a multiplexed proxy-server, designed to work with the database divided to several servers.
  • tempire/MojoExample - Mojolicious example with DBIx::Class schema load, deploy, fixtures, and tests.
  • reyjrar/es-utils - ElasticSearch Utilities
  • omniti-labs/omnipitr - Advanced WAL File Management Tools for PostgreSQL
  • GDSSecurity/PadBuster - Automated script for performing Padding Oracle attacks
  • openresty/rds-json-nginx-module - An nginx output filter that formats Resty DBD Streams generated by ngx_drizzle and others to JSON
  • zaf/asterisk-speech-recog - Speech recognition script for Asterisk that uses google's speech engine.
  • Ibmurai/Markdown.codaplugin - A Markdown plugin for Coda.
  • oetiker/SmokePing - The Active Monitoring System
  • openresty/lua-resty-upload - Streaming reader and parser for http file uploading based on ngx_lua cosocket
  • nriley/Pester - Simple, disposable alarms and timers for OS X.
  • dabockster/Smackbook-Yosemite - Updated Smackbook script for OS X Yosemite
  • cloudflare/lua-resty-logger-socket - Raw-socket-based Logger Library for Nginx (based on ngx_lua)
  • simpl/ngx_mongo - Non-blocking upstream module for Nginx to connect to MongoDB
  • iafan/Hacksby - Description and unofficial implementation of Furby's audio protocol
  • NixOS/hydra - Hydra, the Nix-based continuous build system
  • WolverineFan/YNABLinuxInstall - Install script for YNAB 4 on Linux
  • SPORE/specifications - SPORE specifications
  • xchataqua/xchataqua - An IRC client, OS X native front-end for XChat ( http://itunes.apple.com/app/id447521961 )
  • jfrazelle/dotfiles - My dotfiles
  • ytoolshed/pogo - Pogo is an agent-based system for running interruptive commands safely on thousands of machines in parallel
  • openresty/lua-resty-websocket - WebSocket support for the ngx_lua module (and OpenResty)
  • jzawodn/mytop - a "top" clone for MySQL
  • fonnesbeck/Bios8366 - Advanced Statistical Computing at Vanderbilt University's Department of Biostatistics
  • dbsrgits/dbix-class - Official github remote for git.shadowcat.co.uk DBIx-Class.git
  • bricoleurs/bricolage - Content management and publishing system
  • exflickr/GodAuth - Authentication layer for web app tools
  • JJ/hoborg - A dieselpunk novel with Spanish-created robot hobos in a balcanized America at the beginning of the XX century
  • zigdon/xkcd-Bucket - Bucket is the channel bot for #xkcd
  • jollyjinx/ZFS-TimeMachine - TimeMachine style backup for ZFS
  • atomia/atomiadns - Atomia DNS
  • comotion/VSF - Varnish Security Firewall
  • bgcngm/mtk-tools - Unpack / repack MT65xx/MT83xx boot.img, recovery.img or logo.bin
  • windytan/redsea - Decoder for FM-RDS.
  • tudorconstantin/Mojolicious-Boilerplate - The Web in an Awesome Box
  • openresty/lua-upstream-nginx-module - Nginx C module to expose Lua API to ngx_lua for Nginx upstreams
  • openresty/test-nginx - Data-driven test scaffold for Nginx C module and OpenResty Lua library development
  • mndrix/merge-this - Revision control stress tests
  • brendangregg/HeatMap - Heat map generation tools
  • crucially/riakfuse - Filesystem backed by riak
  • DmitryKoterov/dklab_realsync - dkLab RealSync: replicate developer's files over SSH in realtime
  • xme/pastemon - pastebin.com Content Monitoring Tool
  • ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment Thu, 06 Sep 2018 16:27:35 -0500 https://bioinformaticsonline.com/bookmarks/view/37645/lsc-improving-pacbio-long-read-accuracy-by-short-read-alignment <![CDATA[LSC: Improving PacBio Long Read Accuracy by Short Read Alignment]]>
  • Added Command line argument support.
  • Multi-stage execution modes.
  • Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N.
  • Better compressed intermediate files.
  • Added utilities folder.
  • Added support for multiple short read files.
  • Removed use of configuration file.

    • Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

    ]]>     Abhimanyu Singh     https://bioinformaticsonline.com/bookmarks/view/43799/kast Wed, 23 Feb 2022 08:28:36 -0600 https://bioinformaticsonline.com/bookmarks/view/43799/kast <![CDATA[KAST]]> Perform Alignment-free k-tuple frequency comparisons from sequences. This can be in the form of two input files (e.g. a reference and a query) or a single file for pairwise comparisons to be made.

    Address of the bookmark: https://github.com/martinjvickers/KAST

    ]]>     Neel     https://bioinformaticsonline.com/blog/view/44616/basics-of-blast-programs Fri, 26 Jul 2024 06:04:26 -0500 https://bioinformaticsonline.com/blog/view/44616/basics-of-blast-programs <![CDATA[Basics of BLAST Programs !]]> The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.

    Key Features of BLAST:
    1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

    2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

    3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
    - blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
    - blastp: Compares a protein query sequence against a protein sequence database.
    - blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
    - tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
    - tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

    4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

    5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

    Applications of BLAST:
    - Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
    - Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
    - Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
    - Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

    Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.

    ]]>     BioStar     https://bioinformaticsonline.com/bookmarks/view/34038/quota-synteny-alignment Mon, 31 Jul 2017 04:11:57 -0500 https://bioinformaticsonline.com/bookmarks/view/34038/quota-synteny-alignment <![CDATA[Quota synteny alignment]]> Typically in comparative genomics, we can identify anchors, chain them into syntenic blocks and interpret these blocks as derived from a common descent. However, when comparing two genomes undergone ancient genome duplications (plant genomes in particular), we have large number of blocks that are not orthologous, but are paralogous. This has forced us sometimes to use ad-hoc rules to screen these blocks. So the question is: given the expected depth (quota) along both x- and y-axis, select a subset of the anchors with maximized total score.

    Address of the bookmark: https://github.com/tanghaibao/quota-alignment

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/34571/mugsy-multiple-whole-genome-alignment-tool Fri, 08 Dec 2017 17:41:14 -0600 https://bioinformaticsonline.com/bookmarks/view/34571/mugsy-multiple-whole-genome-alignment-tool <![CDATA[Mugsy: multiple whole genome alignment tool]]> Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

    To cite Mugsy, use:

    Angiuoli SV and Salzberg SL. Mugsy: Fast multiple alignment of closely related whole genomes.Bioinformatics 2011 27(3):334-4

    Address of the bookmark: http://mugsy.sourceforge.net/

    ]]>     Jit     https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads Tue, 08 May 2018 04:27:22 -0500 https://bioinformaticsonline.com/bookmarks/view/36512/hisat2-a-fast-and-sensitive-alignment-program-for-mapping-next-generation-sequencing-reads <![CDATA[HISAT2: a fast and sensitive alignment program for mapping next-generation sequencing reads]]> HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). Based on an extension of BWT for graphs [Sirén et al. 2014], we designed and implemented a graph FM index (GFM), an original approach and its first implementation to the best of our knowledge. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). 

    more at https://ccb.jhu.edu/software/hisat2/index.shtml

    Address of the bookmark: https://github.com/infphilo/hisat2

    ]]>     Rahul Nayak     https://bioinformaticsonline.com/bookmarks/view/36846/gblocks-eliminates-poorly-aligned-positions-and-divergent-regions-of-a-dna-or-protein-alignment Sat, 02 Jun 2018 07:36:05 -0500 https://bioinformaticsonline.com/bookmarks/view/36846/gblocks-eliminates-poorly-aligned-positions-and-divergent-regions-of-a-dna-or-protein-alignment <![CDATA[Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment]]> Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its use as simple as possible without loosing the functionality that it is necessary in most of the cases. Other options can be changed in the stand-alone program. You can see here an example output file showing the blocks selected from a protein alignment. Further information can be found in the online documentation. 

    Address of the bookmark: http://molevol.cmima.csic.es/castresana/Gblocks_server.html

    ]]>     Poonam Mahapatra     https://bioinformaticsonline.com/bookmarks/view/39689/msaprobs-parallel-and-accurate-multiple-sequence-alignment Tue, 09 Jul 2019 23:58:44 -0500 https://bioinformaticsonline.com/bookmarks/view/39689/msaprobs-parallel-and-accurate-multiple-sequence-alignment <![CDATA[MSAProbs - Parallel and accurate multiple sequence alignment]]> MSAProbs is a well-established state-of-the-art multiple sequence alignment algorithm for protein sequences. The design of MSAProbs is based on a combination of pair hidden Markov models and partition functions to calculate posterior probabilities. Assessed using the popular benchmarks: BAliBASE, PREFAB, SABmark and OXBENCH, MSAProbs achieves statistically significant accuracy improvements over the existing top performing aligners, including ClustalW, MAFFT, MUSCLE, ProbCons and Probalign. In addition, MSAProbs is optimized for shared-memory CPUs by employing a multi-threaded design, and further parallelized for distributed-memory systems using MPI to overcome high memory overhead barrier and achieve good parallel and data-size scalability.

    Address of the bookmark: http://msaprobs.sourceforge.net/homepage.htm#latest

    ]]>     Neel     https://bioinformaticsonline.com/bookmarks/view/40711/vg-variation-graph-data-structures-interchange-formats-alignment-genotyping-and-variant-calling-methods Tue, 28 Jan 2020 03:53:24 -0600 https://bioinformaticsonline.com/bookmarks/view/40711/vg-variation-graph-data-structures-interchange-formats-alignment-genotyping-and-variant-calling-methods <![CDATA[VG: variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods]]> Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of:

    • nodes, which are labeled by sequences and ids
    • edges, which connect two nodes via either of their respective ends
    • paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges

    Address of the bookmark: https://github.com/vgteam/vg

    ]]>     Jit