<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/36852?offset=10 https://bioinformaticsonline.com/bookmarks/view/39869/mfannot-a-program-for-the-annotation-of-mitochondrial-and-plastid-genomes Mon, 26 Aug 2019 11:47:56 -0500 https://bioinformaticsonline.com/bookmarks/view/39869/mfannot-a-program-for-the-annotation-of-mitochondrial-and-plastid-genomes <![CDATA[MFannot : a program for the annotation of mitochondrial and plastid genomes]]> MFannot is a program for the annotation of mitochondrial and plastid genomes

MFannot is a program for the annotation of mitochondrial and plastid genomes. It is a PERL wrapper around a set of diverse, external independent tools.

It makes intense use of RNA/intron detection tools including HMMER, Exonerate, Erpin and others.

http://megasun.bch.umontreal.ca/cgi-bin/mfannot/mfannotInterface.pl

Address of the bookmark: https://github.com/BFL-lab/Mfannot

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42357/irscope-an-online-program-to-visualize-the-junction-sites-of-chloroplast-genomes Wed, 25 Nov 2020 19:44:46 -0600 https://bioinformaticsonline.com/bookmarks/view/42357/irscope-an-online-program-to-visualize-the-junction-sites-of-chloroplast-genomes <![CDATA[IRscope: an online program to visualize the junction sites of chloroplast genomes]]> eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences.

Address of the bookmark: https://sites.google.com/g.hmc.edu/empress/home

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44445/ppanggolin-depicting-microbial-species-diversity-via-a-partitioned-pangenome-graph-of-linked-neighbors Thu, 01 Feb 2024 00:24:32 -0600 https://bioinformaticsonline.com/bookmarks/view/44445/ppanggolin-depicting-microbial-species-diversity-via-a-partitioned-pangenome-graph-of-linked-neighbors <![CDATA[PPanGGOLiN: Depicting microbial species diversity via a Partitioned PanGenome Graph Of Linked Neighbors]]> PPanGGOLiN (Gautreau et al. 2020) is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species.

A complete documentation is available here.

logo

Address of the bookmark: https://github.com/labgem/PPanGGOLiN

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/37830/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing Thu, 04 Oct 2018 05:23:59 -0500 https://bioinformaticsonline.com/bookmarks/view/37830/nquire-a-statistical-framework-for-ploidy-estimation-using-next-generation-sequencing <![CDATA[nQuire: a statistical framework for ploidy estimation using next generation sequencing]]> nQuire provides a statistical framework to study organisms with intraspecific variation in ploidy. nQuire is likely to be useful in epidemiological studies of pathogens, artificial selection experiments, and for historical or ancient samples where intact nuclei are not preserved. It is implemented as a stand-alone Linux command line tool in the C programming language and is available at https://github.com/clwgg/nQuireunder the MIT license.

Address of the bookmark: https://github.com/clwgg/nQuireunder

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40549/mgse-mapping-based-genome-size-estimation Fri, 17 Jan 2020 02:11:43 -0600 https://bioinformaticsonline.com/bookmarks/view/40549/mgse-mapping-based-genome-size-estimation <![CDATA[MGSE: Mapping-based Genome Size Estimation]]> MGSE can harness the power of files generated in genome sequencing projects to predict the genome size. Required are the FASTA file containing a high continuity assembly and a BAM file with all available reads mapped to this assembly. The script construct_cov_file.py (https://doi.org/10.1186/s12864-018-5360-z) allows the generation of a COV file based on the (sorted) BAM file (also possible via MGSE directly). Next, this COV file can be used by MGSE to calculate the coverage in provided reference regions and to calculate the total number of mapped bases. Both values are subjected to the genome size estimation. Providing accurate reference regions is crucial for this genome size estimation.

Address of the bookmark: https://github.com/bpucker/MGSE

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/44327/homologizer-phylogenetic-phasing-of-gene-copies-into-polyploid-subgenomes Sat, 03 Jun 2023 19:19:10 -0500 https://bioinformaticsonline.com/bookmarks/view/44327/homologizer-phylogenetic-phasing-of-gene-copies-into-polyploid-subgenomes <![CDATA[homologizer: Phylogenetic phasing of gene copies into polyploid subgenomes]]> This tutorial describes the usage of homologizer to phase gene copies into polyploid subgenomes. The tutorial is an abbreviated version of a soon-to-be published paper in Methods in Molecular Biology. Please see that paper for many more details and practical considerations for running homologizer analyses. If you use homologizer, please cite the paper in which we first describe the method:

  • Freyman, W.A., Johnson, M.G., and C.J. Rothfels. 2022. Homologizer: phylogenetic phasing of gene copies into polyploid subgenomes. bioRxiv 2020.10.22.351486v4

homologizer is implemented in RevBayes. Please see http://revbayes.com to download and install RevBayes. For users without previous RevBayes experience, we recommend the tutorials at http://revbayes.com.

Address of the bookmark: https://github.com/wf8/homologizer

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/36360/dendropy-a-python-library-for-phylogenetic-computing Mon, 23 Apr 2018 05:49:50 -0500 https://bioinformaticsonline.com/bookmarks/view/36360/dendropy-a-python-library-for-phylogenetic-computing <![CDATA[DendroPy: a Python library for phylogenetic computing]]> DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting “glue” that assembles and drives such pipelines.

The primary home page for DendroPy, with detailed tutorials and documentation, is at:

DendroPy is also hosted in the official Python repository:

Requirements and Installation

DendroPy 4.x runs under Python 3 (all versions > 3.1) and Python 2 (Python 2.7 only).

You can install DendroPy by running:

 

More information is available here:

Address of the bookmark: https://pypi.org/project/DendroPy/

]]> Seema Singh https://bioinformaticsonline.com/bookmarks/view/44513/mike-an-ultrafast-assembly-and-alignment-free-approach-for-phylogenetic-tree-construction Mon, 08 Apr 2024 06:19:52 -0500 https://bioinformaticsonline.com/bookmarks/view/44513/mike-an-ultrafast-assembly-and-alignment-free-approach-for-phylogenetic-tree-construction <![CDATA[MIKE: an ultrafast, assembly-, and alignment-free approach for phylogenetic tree construction]]> MIKE (MinHash-based k-mer algorithm). This algorithm is designed for the swift calculation of the Jaccard coefficient directly from raw sequencing reads and enables the construction of phylogenetic trees based on the resultant Jaccard coefficient. Simulation results highlight the superior speed of MIKE compared to existing state-of-the-art methods. We used MIKE to reconstruct a phylogenetic tree, incorporating 238 yeast, 303 Zea, 141 Ficus, 67 Oryza, and 43 Saccharum spontaneum samples. MIKE demonstrated accurate performance across varying evolutionary scales, reproductive modes, and ploidy levels, proving itself as a powerful tool for phylogenetic tree construction.

Address of the bookmark: https://github.com/Argonum-Clever2/mike

]]> Abhi 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/opportunity/view/44407/mopga-2024-visiting-fellowship-program-for-early-career-researchers Fri, 10 Nov 2023 02:30:22 -0600 <![CDATA[MOPGA 2024 Visiting Fellowship Program for Early Career Researchers]]> France, as a major player in the fight against climate change and guarantor of the spirit of the Paris Agreement, is launching a new MOPGA visiting fellowship program geared towards strengthening scientific contributions to climate change issues raised by the COPs.

    This seventh Make Our Planet Great Again (MOPGA) call for applications is intended to welcome at least 40 early career researchers wishing to carry out their research in France. The program is funded by the French Ministry for Europe and Foreign Affairs, in collaboration with the French Ministry for Higher Education and Research, and implemented by Campus France.

    The MOPGA 2024 Visiting Fellowship Program for Early Career Researchers will support researchers working on topics listed in the "Research Themes" section.

    More at https://www.campusfrance.org/en/mopga-2024

    ]]>