Lab https://www.ieo.it/en/RESEARCH/People/Researchers/Pasini-Diego/

Gene expression and protein expression patterns between normal and non-normal tissues is a growing area of research that may lead to the identification of candidate genes for understanding the etiology of common, complex diseases.

Lab homepage @ http://ritchielab.psu.edu/ritchielab/

Align/Assemble to a reference
BFAST - Blat-like Fast Accurate Search Tool. Written by Nils Homer, Stanley F. Nelson and Barry Merriman at UCLA.
Bowtie - Ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of 25 million reads per hour on a typical workstation with 2 gigabytes of memory. Uses a Burrows-Wheeler-Transformed (BWT) index. Link to discussion thread here. Written by Ben Langmead and Cole Trapnell. Linux, Windows, and Mac OS X.
BWA - Heng Lee's BWT Alignment program - a progression from Maq. BWA is a fast light-weighted tool that aligns short sequences to a sequence database, such as the human reference genome. By default, BWA finds an alignment within edit distance 2 to the query sequence. C++ source.
ELAND - Efficient Large-Scale Alignment of Nucleotide Databases. Whole genome alignments to a reference genome. Written by Illumina author Anthony J. Cox for the Solexa 1G machine.
Exonerate - Various forms of pairwise alignment (including Smith-Waterman-Gotoh) of DNA/protein against a reference. Authors are Guy St C Slater and Ewan Birney from EMBL. C for POSIX.
GenomeMapper - GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. A tool created by the 1001 Genomes project. Source for POSIX.
GMAP - GMAP (Genomic Mapping and Alignment Program) for mRNA and EST Sequences. Developed by Thomas Wu and Colin Watanabe at Genentec. C/Perl for Unix.
gnumap - The Genomic Next-generation Universal MAPper (gnumap) is a program designed to accurately map sequence data obtained from next-generation sequencing machines (specifically that of Solexa/Illumina) back to a genome of any size. It seeks to align reads from nonunique repeats using statistics. From authors at Brigham Young University. C source/Unix.
MAQ - Mapping and Assembly with Qualities (renamed from MAPASS2). Particularly designed for Illumina with preliminary functions to handle ABI SOLiD data. Written by Heng Li from the Sanger Centre. Features extensive supporting tools for DIP/SNP detection, etc. C++ source
MOSAIK - MOSAIK produces gapped alignments using the Smith-Waterman algorithm. Features a number of support tools. Support for Roche FLX, Illumina, SOLiD, and Helicos. Written by Michael Strömberg at Boston College. Win/Linux/MacOSX
MrFAST and MrsFAST - mrFAST & mrsFAST are designed to map short reads generated with the Illumina platform to reference genome assemblies; in a fast and memory-efficient manner. Robust to INDELs and MrsFAST has a bisulphite mode. Authors are from the University of Washington. C as source.
MUMmer - MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. Released as a package providing an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools. Version 3.0 was developed by Stefan Kurtz, Adam Phillippy, Arthur L Delcher, Michael Smoot, Martin Shumway, Corina Antonescu and Steven L Salzberg - most of whom are at The Institute for Genomic Research in Maryland, USA. POSIX OS required.
Novocraft - Tools for reference alignment of paired-end and single-end Illumina reads. Uses a Needleman-Wunsch algorithm. Can support Bis-Seq. Commercial. Available free for evaluation, educational use and for use on open not-for-profit projects. Requires Linux or Mac OS X.
PASS - It supports Illumina, SOLiD and Roche-FLX data formats and allows the user to modulate very finely the sensitivity of the alignments. Spaced seed intial filter, then NW dynamic algorithm to a SW(like) local alignment. Authors are from CRIBI in Italy. Win/Linux.
RMAP - Assembles 20 - 64 bp Illumina reads to a FASTA reference genome. By Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics). POSIX OS required.
SeqMap - Supports up to 5 or more bp mismatches/INDELs. Highly tunable. Written by Hui Jiang from the Wong lab at Stanford. Builds available for most OS's.
SHRiMP - Assembles to a reference sequence. Developed with Applied Biosystem's colourspace genomic representation in mind. Authors are Michael Brudno and Stephen Rumble at the University of Toronto. POSIX.
Slider- An application for the Illumina Sequence Analyzer output that uses the probability files instead of the sequence files as an input for alignment to a reference sequence or a set of reference sequences. Authors are from BCGSC. Paper is here.
SOAP - SOAP (Short Oligonucleotide Alignment Program). A program for efficient gapped and ungapped alignment of short oligonucleotides onto reference sequences. The updated version uses a BWT. Can call SNPs and INDELs. Author is Ruiqiang Li at the Beijing Genomics Institute. C++, POSIX.
SSAHA - SSAHA (Sequence Search and Alignment by Hashing Algorithm) is a tool for rapidly finding near exact matches in DNA or protein databases using a hash table. Developed at the Sanger Centre by Zemin Ning, Anthony Cox and James Mullikin. C++ for Linux/Alpha.
SOCS - Aligns SOLiD data. SOCS is built on an iterative variation of the Rabin-Karp string search algorithm, which uses hashing to reduce the set of possible matches, drastically increasing search speed. Authors are Ondov B, Varadarajan A, Passalacqua KD and Bergman NH.
SWIFT - The SWIFT suit is a software collection for fast index-based sequence comparison. It contains: SWIFT — fast local alignment search, guaranteeing to find epsilon-matches between two sequences. SWIFT BALSAM — a very fast program to find semiglobal non-gapped alignments based on k-mer seeds. Authors are Kim Rasmussen (SWIFT) and Wolfgang Gerlach (SWIFT BALSAM)
SXOligoSearch - SXOligoSearch is a commercial platform offered by the Malaysian based Synamatix. Will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Web Portal. OS independent.
Vmatch - A versatile software tool for efficiently solving large scale sequence matching tasks. Vmatch subsumes the software tool REPuter, but is much more general, with a very flexible user interface, and improved space and time requirements. Essentially a large string matching toolbox. POSIX.
Zoom - ZOOM (Zillions Of Oligos Mapped) is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis. ZOOM is developed to be highly accurate, flexible, and user-friendly with speed being a critical priority. Commercial. Supports Illumina and SOLiD data.
NCGR uses GMAP (http://www.gene.com/share/gmap/) to alignment Solexa reads. GMAP is free, though.
Exonerate (http://www.ebi.ac.uk/~guy/exonerate/)
MUMmer (http://mummer.sourceforge.net/)
The mapping short reads called gnumap (http://dna.cs.byu.edu/gnumap/) made to increase the accuracy with duplicate matches. Open source, creates viewable output (with Affy's Integrated Genome Browser), and produces results very similar to novocraft's.
SOCS (short oligonucleotides in color space)
BFAST https://secure.genome.ucla.edu/index.php/BFAST

De novo Align/Assemble
ABySS - Assembly By Short Sequences. ABySS is a de novo sequence assembler that is designed for very short reads. The single-processor version is useful for assembling genomes up to 40-50 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes. By Simpson JT and others at the Canada's Michael Smith Genome Sciences Centre. C++ as source.
ALLPATHS - ALLPATHS: De novo assembly of whole-genome shotgun microreads. ALLPATHS is a whole genome shotgun assembler that can generate high quality assemblies from short reads. Assemblies are presented in a graph form that retains ambiguities, such as those arising from polymorphism, thereby providing information that has been absent from previous genome assemblies. Broad Institute.
Edena - Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. By D. Hernandez, P. François, L. Farinelli, M. Osteras, and J. Schrenzel. Linux/Win.
EULER-SR - Short read de novo assembly. By Mark J. Chaisson and Pavel A. Pevzner from UCSD (published in Genome Research). Uses a de Bruijn graph approach.
MIRA2 - MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required.
SEQAN - A Consistency-based Consensus Algorithm for De Novo and Reference-guided Sequence Assembly of Short Reads. By Tobias Rausch and others. C++, Linux/Win.
SHARCGS - De novo assembly of short reads. Authors are Dohm JC, Lottaz C, Borodina T and Himmelbauer H. from the Max-Planck-Institute for Molecular Genetics.
SSAKE - The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a genomics application for aggressively assembling millions of short nucleotide sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix tree. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux.
SOAPdenovo - Part of the SOAP suite. See above.
VCAKE - De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE.
Velvet - Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI).
SOAP (http://soap.genomics.org.cn) by Ruiqiang Li, as has been pointed by ECO.
Euler-SR (Euler-Short Reads Assembly, http://euler-assembler.ucsd.edu/portal/) by Mark J. Chaisson and Pavel A. Pevzner from UCSD. (published in Genome Research)
RMAP (A program for mapping Solexa reads, http://rulai.cshl.edu/rmap/) by Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics)
Short read aligner called Bowtie (http://bowtie-bio.sourceforge.net/) designed for fast mapping of Illumina reads

SNP/Indel Discovery
ssahaSNP - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac
PolyBayesShort - A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College. Linux-64 and Linux-32.
PyroBayes - PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequences. Developers at Boston College.
Maq is also able to find SNPs with its own alignment. It has a graphical viewer, but again for its own alignment format.
SSAHA has been optimized for short-reads, too. But yes, SSAHASNP appears in your "SNP/INDEL discovery" category.

Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database
EagleView - An information-rich genome assembler viewer. EagleView can display a dozen different types of information including base quality and flowgram signal. Developers at Boston College.
LookSeq - LookSeq is a web-based application for alignment visualization, browsing and analysis of genome sequence data. LookSeq supports multiple sequencing technologies, alignment sources, and viewing modes; low or high-depth read pileups; and easy visualization of putative single nucleotide and structural variation. From the Sanger Centre.
MapView - MapView: visualization of short reads alignment on desktop computer. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China. Linux.
SAM - Sequence Assembly Manager. Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developers are Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones at Canada's Michael Smith Genome Sciences Centre. MySQL backend and Perl-CGI web-based frontend/Linux.
STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here
XMatchView - A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre. Python/Win or Linux.

Counting e.g. CHiP-Seq, Bis-Seq, CNV-Seq
BS-Seq - The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning" Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX.
CHiPSeq - Program used by Johnson et al. (2007) in their Science publication
CNV-Seq - CNV-seq, a new method to detect copy number variation using high-throughput sequencing. Chao Xie and Martti T Tammi at the National University of Singapore. Perl/R.
FindPeaks - perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest. Original algorithm by Matthew Bainbridge, in collaboration with Gordon Robertson. Current code and implementation by Anthony Fejes. Authors are from the Canada's Michael Smith Genome Sciences Centre. JAVA/OS independent. Latest versions available as part of the Vancouver Short Read Analysis Package
MACS - Model-based Analysis for ChIP-Seq. MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. Written by Yong Zhang and Tao Liu from Xiaole Shirley Liu's Lab.
PeakSeq - PeakSeq: Systematic Scoring of ChIP-Seq Experiments Relative to Controls. a two-pass approach for scoring ChIP-Seq data relative to controls. The first pass identifies putative binding sites and compensates for variation in the mappability of sequences across the genome. The second pass filters out sites that are not significantly enriched compared to the normalized input DNA and computes a precise enrichment and significance. By Rozowsky J et al. C/Perl.
QuEST - Quantitative Enrichment of Sequence Tags. Sidow and Myers Labs at Stanford. From the 2008 publication Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. (C++)
SISSRs - Site Identification from Short Sequence Reads. BED file input. Raja Jothi @ NIH. Perl.
SeqMap (http://biogibbs.stanford.edu/~jiangh/SeqMap/) - work like ELand, can do 3 or more bp mismatches and also insdel
ChIPSeq analysis is:  http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/

See also this thread for ChIP-Seq, until I get time to update this list.

Alternate Base Calling
Rolexa - R-based framework for base calling of Solexa data. Project publication
Alta-cyclic - "a novel Illumina Genome-Analyzer (Solexa) base caller"

Transcriptomics
ERANGE - Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq. Supports Bowtie, BLAT and ELAND. From the Wold lab.
G-Mo.R-Se - G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models. First, candidate exons are built directly from the positions of the reads mapped on the genome (without any ab initio assembly of the reads), and all the possible splice junctions between those exons are tested against unmapped reads. From CNS in France.
MapNext - MapNext: A software tool for spliced and unspliced alignments and SNP detection of short sequence reads. From the Evolutionary Genomics Lab at Sun-Yat Sen University, China.
QPalma - Optimal Spliced Alignments of Short Sequence Reads. Authors are Fabio De Bona, Stephan Ossowski, Korbinian Schneeberger, and Gunnar Rätsch. A paper is available.
RSAT - RSAT: RNA-Seq Analysis Tools. RNASAT is developed and maintained by Hui Jiang at Stanford University.
TopHat - TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. TopHat is a collaborative effort between the University of Maryland and the University of California, Berkeley
NGS-Trex: Next Generation Sequencing Transcriptome profile explorer http://www.biomedcentral.com/1471-2105/14/S7/S10

Reference

Illumina has a software list: http://www.illumina.com/pagesnrn.ilmn?ID=245.

Some softwares in his blog (http://www.fejes.ca/labels/DNA.html)

http://seqanswers.com/wiki/Software

Note that the information on this page is targeted at end-users. For developers, the source code, building instructions and implementation/development resources are available on GitHub.

The Picard toolkit is open-source under the MIT license and free for all uses.

Enjoy!

Address of the bookmark: http://broadinstitute.github.io/picard/

GAEMR’s analysis philosophy is centered on contiguity, correctness, and completeness -- how many pieces in an assembly composed of, how well those pieces accurately represent the genome sequenced, and how much of that genome is represented by those pieces. By performing over twenty different analyses based on these principles, GAEMR gives a clear picture of the condition of a genome assembly. 

Address of the bookmark: https://www.broadinstitute.org/software/gaemr/

Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.

http://www.comp.nus.edu.sg/~wongls/projects/orthoGNC/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S1672022917301663

3D-Dock Suite

Global rigid search: FFTShape complementarity and electrostatics

Re-scoring and clustering. Refinement of interface side-chains

3D-Garden

Global rigid search in ensamble

Shape complementarity and Lennard–Jones potential

Side chain and backbone dihedral refinement

DOT

Global rigid search: FFTShape complementarity, electrostatics and VDWNone

Escher NG

Global rigid searchShape complementarity, hydrogen bonds and electrostatic

Integrated in VEGA

GRAMM 

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potential

Clustering of conformations

GRAMM-X 

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potentialminimization and re-scoring with multiple filters

HEX

Global rigid search: Fourier correlation of spherical harmonics

Shape complementarity

HADDOCK

Global rigid searchElectrostatic ,VDW and desolvation energy termsMD simulated annealing refinement . Filtering based on external data. 

ICM

Global rigid search: Monte CarloEmpirical scoring function

Clustering and selection of conformations. Refinement of interface side-chains and re-scoring

MolFit 

Global rigid search: FFTShape complementarity

Clustering of good solutions, filtering using a priori information and small, local rigid rotations around selected conformations

PatchDock

Global rigid searchShape complementarity and atomic desolvation energy

Clustering of conformations

PyDock

Global rigid search:FFTShape complementarity

rescoring by binding electrostatics and desolvation energy

RosettaDock

Local rigid search: Monte Carlo with low and high resolution structure representation levels

Different scoring parameters for the different resolutions 

ZDOCK

Global rigid search: FFTShape complementarity, desolvation energy, and electrostatics.

Energy minimization and re-scoringFree for academics

Point to note:

The proper treatment of flexibility in protein–protein docking is still an active field of research. You first should analyzed your proteins in order to define their conformational space and then choose the most suitable method for your docking problem.

Address of the bookmark: https://github.com/PapenfussLab/gridss

• major/MySQLTuner-perl - MySQLTuner is a script written in Perl that will assist you with your MySQL configuration and make recommendations for increased performance and stability.
• kraih/mojo - Mojolicious - Perl real-time web framework
• petdance/ack2 - ack 2.0 is a greplike tool optimized for programmers searching large heterogeneous trees of source code.
• rsnapshot/rsnapshot - a tool for backing up your data using rsync (if you want to get help, use https://lists.sourceforge.net/lists/listinfo/rsnapshot-discuss)
• fletcher/MultiMarkdown - Expanded perl version of John Gruber's original Markdown --- No longer under active development since MMD 3
• PerlDancer/Dancer - The easiest way to write web applications with Perl (Perl web micro-framework)
• duckduckgo/zeroclickinfo-goodies - DuckDuckGo Instant Answers based on Perl & JavaScript
• sjdy521/Mojo-Webqq - 使用Perl语言（不会没关系）编写的smartqq/webqq客户端框架（非GUI），可通过插件提供基于HTTP协议的api接口供其他语言或系统调用
• chromatic/modern_perl_book - Modern Perl: the book
• gugod/App-perlbrew - Manage perl installations in your $HOME
• muennich/urxvt-perls - Perl extensions for the rxvt-unicode terminal emulator
• sjdy521/Mojo-Weixin - 使用Perl语言（不会没关系）编写的微信/weixin/wechat客户端框架（非GUI），可通过插件提供基于HTTP协议的api接口供其他语言或系统调用
• Nordaaker/convos - Better group chat
• mikaku/Monitorix - Monitorix is a free, open source, lightweight system monitoring tool.
• vsespb/mt-aws-glacier - Perl Multithreaded Multipart sync to Amazon Glacier
• skx/sysadmin-util - Tools for Linux/Unix sysadmins.
• perl-carton/carton - Bundler or pip freeze for Perl
• PerlDancer/Dancer2 - Perl Dancer Next Generation (rewrite of Perl Dancer)
• OpenKore/openkore - A free/open source client and automation tool for Ragnarok Online
• hachiojipm/awesome-perl - A curated list of awesome Perl frameworks and libraries. Come on Pull Requests!
• Perl/perl5 - The Perl 5 language interpreter (MIRROR ONLY)
• fglock/Perlito - Perl 5 and Perl 6 compilers
• miyagawa/Starman - Starman is a high-performance preforking Perl PSGI web server
• ronilaukkarinen/weed - Heavily Xchat inspired beautiful irssi theme.
• trizen/youtube-viewer - A lightweight application for searching and streaming videos from YouTube.
• rakudo/star - Rakudo Star Perl 6 distribution
• GouveaHeitor/nipe - Nipe is a script to make Tor Network your default gateway.
• yuvi/gas-preprocessor - Perl script that implements a subset of the GNU as preprocessor that Apple's as doesn't
• mongodb/mongo-perl-driver - Perl driver for the MongoDB
• wireghoul/dotdotpwn - DotDotPwn - The Directory Traversal Fuzzer
• oysttyer/oysttyer - An interactive console text-based command-line Twitter client written in Perl
• bioperl/bioperl-live - Core BioPerl 1.x code
• tadzik/rakudobrew - Perl 6 installation manager
• fwaeytens/dnsenum - dnsenum is a perl script that enumerates DNS information
• evalEmpire/perl5i - A single module to fix as much of Perl 5 as possible in one go
• shirkdog/pulledpork - Pulled Pork for Snort and Suricata rule management (from Google code)
• hollie/misterhouse - Perl open source home automation program. It's fun, it's free, and it's entirely geeky.
• stevan/p5-mop-redux - A(nother) MOP for Perl 5
• stevan/p5-mop-original - A MOP for Perl 5
• pgbackrest/pgbackrest - Reliable PostgreSQL Backup & Restore
• gempesaw/Selenium-Remote-Driver - Perl Bindings to the Selenium Webdriver server
• libwww-perl/libwww-perl - The libwww-perl collection is a set of Perl modules which provides a simple and consistent application programming interface to the World-Wide Web. The main focus of the library is to provide classes and functions that allow you to write WWW clients. The library also contain modules that are of more general use and even classes that help you implement simple HTTP servers.
• andk/pause - Perl authors upload server
• miyagawa/remedie - perl based pluggable media center application
• mojomojo/mojomojo - A Catalyst & DBIx::Class powered Wiki.
• xslate/p5-Text-Xslate - Scalable template engine for Perl5
• moose/Moose - Official repository for Moose
• llaera/slowloris.pl - A new DOS Perl Programm
• colorgcc/colorgcc - colorgcc is a perl script to colorize gcc output. I'm collecting random patches and changes
• bbusschots/hsxkpasswd - A Perl module and terminal command for generating secure memorable passwords inspired by the fabulous XKCD web comic and Steve Gibson's Password Hay Stacks. This is the library that powers www.xkpasswd.net
• Test-More/test-more - Test2, Test::More, Test::Simple and Test::Builder Perl modules for writing tests
• smtpd/qpsmtpd - qpsmtpd is a flexible smtpd daemon written in Perl
• perseo22/pacmanager - Perl/GTK Gnome SSH GUI on steroids. Configure SSH/Telnet connections: users, passwords, EXPECT regular expressions, macros, ...
• noxxi/p5-ssl-tools - various standalone perl scripts
• chromatic/little_plack_book - Using Plack and PSGI in Modern Perl Web Applications
• mschilli/log4perl - Log4j Implementation For Perl
• centreon/centreon-plugins - Collection of plugins for softwares compatible with Nagios plugins
• fayland/perl-net-github - Perl interface to GitHub
• Perl-Critic/Perl-Critic - The leading static analyzer for Perl. Configurable, extensible, powerful.
• abw/Template2 - Perl Template Toolkit v2
• stf-storage/stf - STF - Distributed Object Storage (Perl/MySQL/(Q4M|TheSchwartz|Resque|Redis)/Memcached)
• PerlRedis/perl-redis - Perl binding for Redis database
• pplu/aws-sdk-perl - A community AWS SDK for Perl Programmers
• sveinbjornt/Data-URL-Toolkit - Various tools for working with Data URLs, incl. web application (http://dataurl.net), Mac OS X GUI app, command line tool, Perl modules and Apache module.
• perl6/ecosystem - Perl 6 ecosystem -- modules and more
• moznion/Perl-Lint - Yet Another Perl Source Code Linter
• briandfoy/PerlPowerTools - Perl Power Tools
• gshank/html-formhandler - a Perl Moose HTML form handler
• mskcc/vcf2maf - Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
• miyagawa/web-scraper - Perl web scraping toolkit
• semifor/Net-Twitter - A Perl interface to the Twitter APIs
• kraih/minion - Perl job queue
• fletcher/MultiMarkdown-CMS - Package to assist with publishing a web site using MMD and a few perl scripts
• rcaputo/poe - POE is a portable perl multitasking and networking framework for any event loop.
• kraih/mango - Pure-Perl non-blocking I/O MongoDB driver
• dreamwidth/dw-free - Dreamwidth's open source repository
• garu/Data-Printer - colored pretty-print of Perl data structures and objects
• PerlGameDev/SDL - Rehashing the old perl SDL binding on cpan.org
• yanick/Template-Mustache - Drawing Mustaches on Perl, for fun and profit
• pjcj/Devel--Cover - Code coverage metrics for Perl
• sebthebert/Octopussy - Octopussy - Open Source Log Management Solution
• gphat/chart-clicker - Extensible, Beautiful Charts for Perl
• audreyt/lingua-sinica-perlyuyan - Perl in Classical Chinese in Perl
• book/perlsecret - The perl secret operators
• OCSInventory-NG/OCSInventory-Server - Communication server of OCS Inventory
• jmapio/jmap-perl - JMAP Proxy implemented in Perl
• fusioninventory/fusioninventory-agent - FusionInventory Agent
• samm-git/jvpn - Perl script to connect to the Juniper VPN with Host Checker enabled
• perl11/cperl - a perl5 with classes, types, compilable, company friendly, security
• kbh3rd/shptosvg - Shapefile to SVG renderer in Perl
• famzah/langs-performance - C++ vs. Python vs. Perl vs. PHP vs. Java vs. NodeJS vs. Go vs. Ruby performance benchmark
• agentzh/old-openresty - Obsolete 1st generation of OpenResty written mostly in Perl. Please check out the new OpenResty based on Nginx and Lua instead.
• kraih/mojo-pg - Mojolicious PostgreSQL
• jmcnamara/excel-writer-xlsx - Perl module to create Excel XLSX files.
• plainblack/webgui - A free open source content management system and web application framework. The most widely deployed mod_perl application on the planet.
• mharsch/arcstat - uses Perl to extract, format, and display kstats from the ZFS ARC
• thaljef/Pinto - Curate your own repository of Perl modules
• rcaputo/reflex - Reflex is a class library for writing reactive Perl programs. It provides base classes for reactive objects, and specific subclasses for various tasks.
• memowe/contenticious - A simple file based "CMS" on Mojo steroids!
• rjust/defects4j - A Database of Existing Faults to Enable Controlled Testing Studies for Java
• elastic/elasticsearch-perl - New Perl low-level client
• blogs-perl-org/blogs.perl.org - Templates and stuff for the blogs.perl.org web site
• agordon/dancer_bootstrap_fontawesome_template - A template for quick-starting applications using Perl's Dancer, Twitter's Bootstrap and Font-Awesome.
• fletcher/SimplenoteSync - perl routine to sync folder of text files with your notes on Simplenote
• tobert/perl-ssh-tools - A more capable DSH / cluster ssh suite
• skx/dhcp.io - Dynamic DNS - Via Redis, Perl, and Amazon Route53.
• perl6/mu - Universal Perl 6 repository (formerly called "pugs repository")
• perl5-dbi/dbi - DBI - The Perl 5 Database Interface
• masterzen/mysql-snmp - Net-SNMP perl agent for monitoring MySQL servers
• rizen/Facebook-Graph - A perl module to help navigate the intricacies of the Facebook Graph API.
• lhost/sendxmpp - perl-script to send xmpp (jabber), similar to what mail(1) does for mail.
• Real-Gecko/Filemin - File manager for Webmin written completely in perl
• preaction/Statocles - Static website CMS
• jonswar/perl-mason - Mason 2
• davorg/perlwebbook - A book. About Perl. And the Web.
• plu/Pithub - Perl Github v3 API
• motemen/Wight - Communicate with PhantomJS in Perl (Capybara+Poltergeist to Perl)
• ingydotnet/pegex-pm - Pegex Parser for Perl
• ewels/ClusterFlow - A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
• denny/ShinyCMS - ShinyCMS is an open source CMS built in Perl using the Catalyst framework.
• nassosoassos/sail_align - SailAlign is an open-source software toolkit for robust long speech-text alignment implementing an adaptive, iterative speech recognition and text alignment scheme that allows for the processing of very long (and possibly noisy) audio and is robust to transcription errors. It is mainly written as a perl library but its functionality also depends on freely available software, namely HTK, srilm and sclite.
• masak/web - A Perl 6 web framework
• agentzh/perl-systemtap-toolkit - Real-time analyzing and diagnosing tools for perl 5 based on SystemTap
• vti/showmethedesktop - Perl + VNC + WebSockets + HTML5 Canvas
• vmbrasseur/Perl_Companies - A list of companies which use Perl. Initially generated from postings to jobs.perl.org.
• perlorg/perlweb - Various perl.org websites
• norbu09/Net--Dropbox - perl interface to the Dropbox API
• line/line-bot-sdk-perl - LINE::Bot::API - SDK of the LINE Messaging API for Perl
• ericblue/Perl-FitBit-API - Provides an OO API for fetching fitness data from fitbit.com. Currently there is no official API, however data is retrieved using XML feeds that populate the flash-based charts.
• ericblue/Perl-Belkin-WeMo-API - Perl-Belkin-WeMo-API
• EnlightenedPerlOrganisation/task-kensho - A Glimpse at an Enlightned Perl Distribution
• dasdom/CreateAppStoreBill - A perl script and tex files to create bills for the German tax office from Apple's financial reports.
• plicease/FFI-Platypus - Write Perl bindings to non-Perl libraries with FFI. No XS required.
• ido50/Svsh - Process supervision shell for daemontools, perp, s6 and runit
• skx/templer - A modular extensible static-site-generator written in perl.
• lestrrat/p5-ZMQ - libzmq Perl binding
• jpoliv/wakeonlan - Perl script for waking up computers via Wake-On-LAN magic packets
• dod38fr/config-model - Perl module to create configuration editor wtih semantic validation
• pjlsergeant/test-bdd-cucumber-perl - Test::BDD::Cucumber - Cucumber in Perl
• onishi/perl5-devel-kytprof - Devel::KYTProf - Simple Perl code profiler
• finance-quote/finance-quote - Finance::Quote module for Perl
• fcuny/net-http-spore - Perl implementation for SPORE
• dpavlin/perl-cwmp - Perl ACS server implementing CWMP protocol to manage CPE clients
• abh/pgeodns - Geographic Perl Nameserver
• timbunce/devel-nytprof - Perl Devel::NYTProf
• symkat/Daemon-Control - Daemon::Control - Create init scripts in Perl
• sartak/webmachine-perl - A Perl port of Webmachine
• rhuss/jmx4perl - JMX access tools and modules
• Perl/docker-perl - Dockerfiles for index.docker.io (official Perl Docker image)
• duckduckgo/p5-app-duckpan - DuckDuckHack OpenSource Development Application
• CaptTofu/DBD-mysql - DBD::mysql Perl client driver for the MySQL and MariaDB databases
• beide/Bootimg-scripts - Perl scripts for unpacking and repackaging Android boot.img's. I did not write these, just sharing.
• spezifanta/SteamCalculator-Scripts - Perl scripts, which parses the Valve's Steam store.
• rurban/perl-compiler - B::C - Moved over from googlecode
• pkrumins/perl-tcp-proxy - A simple TCP proxy written in Perl. Uses IO::Socket::INET and IO::Select for multiplexing.
• perl-users-jp/perl-advent-calendar - japanese perl advent calendar - fork 禁止
• Perl-Toolchain-Gang/ExtUtils-MakeMaker - Perl module to make Makefiles and build modules (what backs Makefile.PL)
• msgpack/msgpack-perl - MessagePack serializer implementation for Perl / msgpack.org[Perl]
• kablamo/git-spark - Plot your commit history on the command line with sparklines. A mash up of git and spark and Perl.
• Aralhach/bashobfus - A small bash minifier/obfuscator written in Perl.
• aesuli/Amazon-downloader - Two perl scripts to download and parse Amazon's reviews
• sjdy521/pfqq - 【该项目已停止维护，请关注重构项目: Mojo-Webqq】使用Perl语言编写的webqq客户端框架（非GUI），支持旧版webqq的多重md5带盐登录密码算法以及新版smartqq的md5+rsa+tea+base64组合登录密码算法
• raszi/colorize - Log colorizer perl script
• iinteractive/OX - the hardest working two letters in Perl
• ap/perldoc-complete - A bash completion helper for perldoc
• xsawyerx/perl-android-scripts - Collection of Perl scripts (examples, programs) that run on Android using ASE
• typester/kamaitachi - perl flash media server
• szabgab/perlmaven.com - The source files of the Perl Maven articles
• petdance/perl101 - The source for perl101.org
• acme/git-pureperl - A Pure Perl interface to Git repositories
• vti/text-haml - Haml parser in Perl
• jploski/epic-ide - EPIC - Eclipse Perl Integration (new official repository!)
• jnthn/blizkost - Makes Perl 5 available as if it were just another Parrot language by embedding the Perl 5 interpreter.
• jeroennijhof/pam_script - PAM script module will allow you to execute scripts during authorization, password changes and sessions. This is very handy if your current security application has no pam support but is accessable with perl or other scripts.
• jberger/Zoidberg - A modular perl shell
• hitode909/App-PRT - Command line tool for Perl code refactoring
• fluent/fluent-logger-perl - A structured logger for Fluentd (Perl)
• dann/p5-cpan-packager - CPAN::Packager is a tool to help you make packages from perl modules on CPAN.
• cotto/www-workflowy - unofficial reverse-engineered Perl 5 interface to Workflowy
• Corion/www-mechanize-firefox - The API of WWW::Mechanize, combined with the Javascript-power of Firefox
• cooldaemon/RabbitFoot - An asynchronous and multi channel Perl AMQP client. It uses Coro and AnyEvent::RabbitMQ.
• perlpilot/perl6-docs - Documents relating to Perl 6
• ingydotnet/mo-pm - Perl Micro Objects
• gnp/psh - Perl Shell (psh) — Aspiring to be your primary login shell
• comewalk/google-api-perl-client - Google APIs Client Library for Perl
• CiderWebmail/CiderWebmail - Perl/Catalyst/AJAX based Webmail
• barbie/perl-jam - Perl Jam - a book about organising conferences
• typester/perldojo - online perl testing!
• tsee/ZeroMQ-Perl - Perl interface to 0MQ2
• trizen/obmenu-generator - A fast menu generator for the Openbox Window Manager.
• rjbs/App-Cmd - perl framework for testable, extensible command line apps
• grampajoe/Autodatamosh - Perl script that automatically datamoshes MPEG4-encoded AVI videos.
• xtaran/unburden-home-dir - Automatically unburden $HOME from caches, etc. Useful for $HOME on SSDs, small disks or slow NFS homes. Can be triggered via an hook in /etc/X11/Xsession.d/.
• rjbs/Email-Sender - a perl library for sending email
• kruser/atbat-mongodb - A Perl project that pulls data from MLB's AtBat servers and shoves them into a local MongoDB
• jonswar/perl-chi - Perl CHI distribution
• andrewcmyers/civs - Condorcet Internet Voting System
• sjdy521/Mojo-SinaWeibo - 使用Perl语言编写的新浪微博客户端SDK，通过微博私信和微软小冰进行问答，提供小冰API接口，其他微博功能敬请期待
• perigrin/blawd - Simple Blogging Software in Perl, similar to blosxome or Jekyll
• jacquesg/p5-Git-Raw - Perl bindings to the Git linkable library (libgit2)
• ingydotnet/io-all-pm - All in One Perl IO
• dagolden/Capture-Tiny - (Perl) Capture STDOUT and STDERR from Perl, XS or external programs
• beppu/squatting - A Camping-inspired Web Microframework for Perl
• tempire/perl-google-voice - Perl module to interact with Google::Voice
• njh/perl-net-sdp - Perl Module : Session Description Protocol (rfc2327)
• songzan/perl5-doc - Perldoc Help Chinese Planning
• sisimai/p5-Sisimai - Mail Analyzing Interface for email bounce: A Perl module to parse RFC5322 bounce mails and generating structured data as JSON from parsed results. Formerly known as bounceHammer 4: an error mail analyzer.
• shenwei356/bio_scripts - Practical, reusable scripts for bioinformatics
• mozilla-bteam/bmo - bugzilla.mozilla.org source
• jamadam/mojo-legacy - mojo for Perl-5.8.7
• briandfoy/Learning-Perl-Sample-Files - Extra files for use with Learning Perl
• theory/uri-db - Perl module representing database URIs
• semifor/twirc - Twitter / IRC gateway in perl
• makamaka/JSON - perl implementation of JSON encoder/decoder
• lukec/cpan-selenium-rc-perl - Test-WWW-Selenium Perl Selenium RC Driver
• keeth/Net-OAuth2 - OAuth 2.0 for Perl
• wireghoul/doona - Fork of Bruteforce Exploit Detector
• pjf/autodie - Make functions succeed or die in Perl, with lexical scope.
• PDLPorters/pdl - Scientific computing with Perl
• ewaters/net-amqp - Implementation of the AMQ Protocol in Perl
• demanuel/NewsUP - NewsUP a binary usenet uploader/poster (multiple connections, SSL and NZB).
• ati/ljsm - perl script for LiveJournal blog backup
• vti/underscore-perl - Underscore-perl is a Perl clone of Underscore.js
• techsneeze/dmarcts-report-parser - A Perl based tool to parse DMARC reports from an IMAP mailbox or from the filesystem, and insert the information into a database. ( Formerly known as imap-dmarcts )
• prepan-developers/prepan - Social Reviewing for Perl Modules
• portcullislabs/rdp-sec-check - PERL script to enumerate security settings of an RDP Service (AKA Terminal Services)
• mlawren/githook-perltidy - Run perltidy as a Git pre-commit hook
• miyagawa/xml-atom - XML::Atom perl module
• jric/epubtohtml - A simple perl script to convert epub documents to documents that browsers can natively browse.
• jmcnamara/spreadsheet-writeexcel - Perl module to write Excel binary files
• FormFu/HTML-FormFu - HTML Form Creation, Rendering and Validation Framework. Just define the form, and let FormFu do the all heavy lifting.
• cbbrowne/autodoc - PostgreSQL Autodoc - dumps a Postgres schema in several useful documentary forms
• xen-tools/xen-tools - xen-tools is a collection of simple perl scripts which allow you to easily create new Xen guest domains upon your Xen host server.
• tokuhirom/Test-TCP - Test::TCP for perl
• timbunce/java2perl6 - Parse Java class files and generate corresponding Perl6 Class and Role files
• stoned/pll - Yet another Perl local::lib+cpanm helper script
• stevan/promises-perl - An implementation of Promises in Perl
• oetiker/mrtg - MRTG - Multi Router Traffic Grapher
• monitoring-plugins/monitoring-plugin-perl - Perl module Monitoring::Plugin - Nagios::Plugin
• mirod/xmltwig - XML, the Perl way
• kraih/perl-raptor - Perl 5 Raptor
• KKBOX/mpdnsd-perl - Marco Polo DNS Daemon
• kevinphilp/Perl-gtk3-Tutorial - Some notes on using Gtk3 with Perl
• kesor/p5-cucumber - Cucumber for Perl 5
• Ensembl/ensembl - The Ensembl Core Perl API and SQL schema
• dankogai/p5-encode - Encode - character encodings (for Perl 5.8 or better)
• rocky/Perl-Devel-Trepan - Perl port of trepanning debugger
• rafl/devel-declare - Adding keywords to perl, in perl
• petdance/html-tidy - HTML::Tidy, a Perl wrapper about libtidy
• libwww-perl/URI - The Perl URI module
• leto/math--gsl - Perl interface to the GNU Scientific Library
• jensenja/graphite-snmp-collector - Asynchronous Perl to collect SNMP data to feed into Graphite
• hachi/Perlbal - Perl HTTP Load Balancer
• bucardo/dbdpg - Perl Postgres driver DBD::Pg aka dbdpg
• aki2o/plsense - Omni completion tool for Perl
• zigorou/perl-JSV - JSON Schema implementation for Perl
• worldmind/perlqual - Wrapper for some tests for Perl code quality
• trizen/trizen - Lightweight AUR Package Manager
• tokuhirom/optimize-perl-doc - how to optimize your perl code?
• peterkeen/proclaunch - A pure-perl process management system
• Ovid/DB--Color - Syntax highlighting the Perl debugger
• jpa/Moose-Doc-JA - Perl Moose Documentation In Japanese
• hakobe/Guita - Gist clone for private use written in Perl
• gonzoua/EBook-EPUB - EBook::EPUB perl module for generating EPUB document
• geuma/pDLNA - perl DLNA MediaServer
• dequis/tmux-url-select - Keyboard based URL selector that integrates with tmux
• Blaizer/ModernPerl-sublime - Perl syntax highlighting for Sublime Text that isn't outdated
• aleex42/netapp-cdot-nagios - Nagios-Checks for monitoring NetApp cDOT-Systems via NetApp Perl API
• simmel/urxvt-resize-font - URxvt Perl extension for resizing the font
• pkrumins/social-scraper - Social scraper is a Perl program that scrapes reddit, digg, stumbleupon, delicious, furl, flickr, simpy, boingboing, wired for content that matches the given patterns.
• metomi/fcm - FCM: a modern Fortran build system + wrappers to Subversion for scientific software development
• khrt/Raisin - Raisin - a REST API micro framework for Perl 
• joshua-hull/Reddit-Image-Scraper - Perl script to download imaged hosted at imgur.com linked from a subreddit at reddit.com
• dpavlin/perl-Redis-obsolete - perl binding for Redis database - latest development is in melo's repository
• cho45/Niro - Blogging System for personal use written in Perl.
• acme/net-amazon-s3 - Use the Amazon S3 - Simple Storage Service from Perl
• vti/plack-middleware-socketio - Socket.IO Perl/Plack implementation DEPRECATED USE PocketIO INSTEAD
• textmate/perl.tmbundle - TextMate support for Perl
• sourceperl/mbtget - A simple modbus/TCP client write in pure Perl.
• semifor/net-twitter-lite - A lighter weight (non-Moose) Perl interface to the Twitter API
• kasei/perlrdf - Official releases of RDF::Query may be found on CPAN: http://search.cpan.org/dist/RDF-Query/
• danaj/Math-Prime-Util - Perl (XS) module implementing prime number utilities, including sieves
• AndyA/Test-Harness - Run Perl standard test scripts with statistics
• sni/Monitoring-Livestatus - Livestatus Perl API to access runtime data from Nagios, Icinga and Shinken.
• skx/markdownshare.com - The code behind http://markdownshare.com/
• Perl-Toolchain-Gang/Module-Build - Perl module to configure and build modules (what backs most Build.PLs)
• markstos/CGI--Application - A Perl framework for building reusable web-applications
• lyokato/p5-oauth-lite2 - Perl Library for OAuth 2.0
• KTamas/pflogsumm - postfix stats
• karupanerura/Aniki - The ORM as our great brother.
• jonswar/perl-poet - Perl Poet distribution
• hzhou/MyDef - Programming in the next paradigm -- your way
• houseabsolute/DateTime.pm - A date and time object for Perl
• fayland/perl-lingua-han - all Lingua::Han:: CPAN modules
• eilara/Rx.pl - Microsoft Reactive Extensions clone for Perl
• dams/curses-toolkit - Curses::Toolkit perl module
• adriaandens/fagrant - Vagrant in 100 lines of (Perl) code
• xsawyerx/module-starter - Module::Starter, a tool to help create solid Perl modules from scratch
• Tux/speedtest - Perl CLI for speedtest.net
• tanjiti/perl_tools - perl小工具
• stevan/BreadBoard - Inversion of Control and Dependency Injection for Perl
• salva/p5-Net-OpenSSH - Perl SSH client built on top of OpenSSH
• rudism/NetAuthority - Historical perl code that ran the original NetAuthority.org site
• pssc/squeezy - A command-line utility for controlling squeezebox network audio players via their squeezeserver.
• portcullislabs/udp-proto-scanner - udp-proto-scanner is a Perl script which discovers UDP services by sending triggers to a list of hosts
• perl5-dbi/DBD-mysql - MySQL driver for the Perl5 Database Interface (DBI)
• Ovid/hop - Higher Order Perl modules on the CPAN
• noxxi/p5-io-socket-ssl - IO::Socket::SSL Perl Module
• kingpong/perl-Test-Spec - rSpec-like test system for Perl
• kensanata/oddmuse - A simple wiki engine written in Perl. No database required.
• gugod/Test-Continuous - (Perl) Run your tests suite continusouly when developing.
• grickit/Gambot - Gambot is a modular IRC bot written in Perl.
• grantm/Algorithm-CouponCode - Perl library to generate and validate 'CouponCode' strings
• eserte/bbbike - BBBike
• book/Git-Repository - Perl interface to Git repositories
• tokuhirom/FormValidator-Lite - very lite and fast validation library for perl
• szbalint/WWW--Curl - Perl binding for libcurl
• stevan/p5-MOP - A Meta Object Protocol for Perl 5
• sludin/Protocol-ACME - A perl library that provides a simple interface to writing scripts for cert provisioning with Let's Encrypt.
• rurban/App-perlall - create and work with /usr/local/bin/perl5.*
• Robertof/perl-www-telegram-botapi - Perl implementation of the Telegram Bot API
• ReneNyffenegger/PerlModules - (Very) simple scripts for some Perl modules, intended as copy paste templates.
• Ovid/Role-Basic - Roles in Perl. Nothing else.
• njlg/perl-rethinkdb - A Pure Perl RethinkDB Driver
• naoya/perl-Text-LTSV - Text::LTSV - Labeled Tab Separated Value manipulator
• memcached/perl-Cache-Memcached - Cache::Memcached
• KD8EYF/TRBO-NET - mototrbo perl modules for ARS TMS and LRRP
• holbertonschool/Betty - Holberton-style C code checker written in Perl
• gnustavo/Git-Hooks - Framework for implementing Git (and Gerrit) hooks
• fayland/perl-www-contact - WWW::Contact - Get contacts/addressbook from Web
• do-know/Crypt-LE - Crypt::LE (ZeroSSL project) - Let's Encrypt client and library in Perl for getting free SSL certificates (inc. generating RSA/ECC keys and CSRs). HTTP/DNS verification is supported out of the box, easily extended with plugins.
• briandfoy/cpan-script - (Perl) Interact with CPAN from the command line
• beppu/anyevent-couchdb - a non-blocking CouchDB client for Perl based on jquery.couch.js
• yannk/ControlFreak - a process supervisor in Perl
• typester/object-container-perl - simple object container
• trizen/menutray - An application menu through a GTK+ tray status icon.
• TrackingSoft/Kafka - Perl implementation of Kafka API (official CPAN module)
• sushdm/git_svn_externals - A perl script to clone an SVN repository with externals, using git-svn
• Perl-Toolchain-Gang/Test-Harness - Run Perl standard test scripts with statistics
• openresty/lemplate - OpenResty/Lua template framework implementing Perl's TT2 templating language
• mkjellman/perlcassa - a Perl client for Apache Cassandra
• LudovicRousseau/pcsc-tools - Some tools to be used with smart cards and PC/SC
• liyanage/build-entropy-php - The Perl-based build system used to build the Entropy PHP distribution
• lixmal/keepass4web - An application that serves KeePass database entries on a web frontend
• hakobe/p5-Fiber - Ruby like Fiber on Perl
• gray/webservice-google-reader - Perl interface to the Google Reader API
• fayland/chinese-perl-book - free book in Chinese "Master Perl Today"
• bruceravel/demeter - Process and analyze X-ray Absorption Spectroscopy data using Feff and either Larch or Ifeffit.
• beanz/xpl-perl - Perl modules for the xPL Home Automation Protocol
• atom/language-perl - Perl package for Atom
• ewels/clusterflow - A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.
• diegok/resque-perl - Perl port of the original Ruby library. It's intended to work using the same backend to share tasks and be able to manage the system using ruby's resque-server webapp. Resque is a Redis-backed library for creating background jobs, placing them on multiple queues, and processing them later.
• perl6/specs - Perl 6 language design documents
• trizen/sidef - A modern object-oriented programming language, implemented in Perl.
• audreyt/pugs - A Perl 6 Implementation
• jlord/git-it-electron - A Git-it Desktop App (A Node.js app, not Perl as GH suggests)
• PerlGameDev/SDL_Manual - The Manual for writing Games in Perl using SDL. Part of TPF grant.
• franckcuny/net-http-spore - Perl implementation for SPORE
• houseabsolute/webmachine-perl - A Perl port of Webmachine
• willemdh/check_netapp_ontap - Check NetApp Ontap 
• unobe/perl-wfa - Perl's WWW::Facebook::API Module
• vti/sockjs-perl - SockJS Perl Plack/PSGI implementation
• schwern/Sex - Perl teaches the birds and the bees
• rjray/rpc-xml - A Perl implementation of the XML-RPC specification
• naoya/mapreduce-lite - An experimental implementation of MapReduce for perl
• miyagawa/perl-app-builder - Turns your perl script into .app using Platypus
• leejo/CGI.pm - The CGI.pm perl module
• kngenie/ias3upload - simple Perl script for uploading files to Internet Archive through its S3-like interface
• jsober/Reddit-API - Reddit API for perl
• jizhang/perl-virtualenv - Virtual Environment for Perl
• Ensembl/ensembl-compara - The Ensembl Compara Perl API and SQL schema
• drforr/Perl-Mogrify - Transmogrify Perl5 code to Perl6 with a plugin system
• cooldaemon/AnyEvent-RabbitMQ - An asynchronous and multi channel Perl AMQP client.
• braintree/braintree_perl - Braintree Perl library
• yuki-kimoto/gitweblite - Git repository browser. This is gtiweb.cgi clone to modern perl.
• yanick/Vim-X - Write Perl functions within Vim
• typester/sniffer-rtmp-perl - rtmp sniffer framework
• tonycoz/imager - Imager - image manipulation from perl. This is a mirror only, pull requests will be closed without comment if I ever notice them. Please submit patches (or bugs) via bug-Imager [at] rt.cpan.org
• tobeychris/hipchat-room-message-APIv2 - This is a simple perl script that will use Hipchat's API v2 to message a room after passing in the room name, authentication token and a message. Also includes features for selecting the colour, notifying the room, passing in an html message, using a proxy and using API v1 should you so choose.
• sass/perl-libsass - Perl bindings for libsass (CSS::Sass)
• ranguard/text-vcard - Perl package to edit and create vCard(s) (RFC 2426)
• pkrumins/perl-tcp-proxy2 - Program for my "A TCP Proxy in Perl" article
• PeterMartini/go-perl - Linking in Go code via XS
• petdance/test-www-mechanize - Test::WWW::Mechanize, a Perl object for testing web pages
• perl-ldap/perl-ldap - Perl LDAP client library
• ntruchsess/perl-firmata - Perl implementation of the firmata client. Originally authored by Aki Mimoto (amimoto) this repository was transfered to Norbert Truchsess (ntruchsess) in 02/2013. Anybody willing to contribute is very wellcome! Please submitt pull-requests against branch 'dev'
• mtw/Bio-ViennaNGS - A Perl extension and collection of utilities for Next-Generation Sequencing (NGS) data analysis
• masukomi/jsonpath-perl - Perl port of JSONPath
• livedoor/Sledge - ancient Perl Web Application Framework.
• kernevil/libfilesys-smbclient-perl - Zentyal packaging of libfilesys-smbclient-perl
• ironcamel/App-p - Steroids for your perl one-liners. Does that mean steroids for your steroids? Is that even possible?
• genoo/GenOO - A Modern Perl Framework for High Throughput Sequencing analysis
• gbarr/perl-libnet - perl libnet library
• evernote/evernote-sdk-perl - Evernote SDK for Perl
• elmex/Construder - A 3D Game written in Perl - inspired by Minecraft
• dsully/perl-crypt-openssl-x509 - Perl interface to OpenSSL's X509 module.
• davorg/perlanet - Simple Planet Clone in Perl
• cosimo/TicketServer - Flickr-like Ticket Server implemented with Perl + DBI + MySQL
• robin13/mediathekp - Perl clone of Mediathek
• rjbs/Mail-DeliveryStatus-BounceParser - perl library to parse email bounce messages
• rjbs/Email-MIME - perl library for parsing MIME messages
• Perl-Toolchain-Gang/Software-License - perl representation of common software licenses
• Perl-Toolchain-Gang/ExtUtils-CBuilder - Compile and link C code for Perl modules
• nothingmuch/git-site-perl - Hooks to keep site_perl in git
• miyagawa/cpanmetadb-perl - CPANMetaDB in Starman and Plack with Carmel
• maxmind/MaxMind-DB-Writer-perl - Create MaxMind DB database files
• mattn/p5-Growl-Any - perl module that provide any growl application
• LyonsLab/coge - CoGe (Comparative Genomics) Platform
• hirose31/inspect-perl-proc - get %INC and dump into file
• formalin14/Transformer - A translation system for static websites. It is used to translate the perl.org website.
• duncs/perl-nagios-object - A group of modules for parsing a Nagios configuration and representing it as objects in perl.
• cyberisltd/ProxyDetect - Perl script to detect the existence of transparent proxies
• ct/net-twitter - Net::Twitter, perl interface to twitter.com
• CpanelInc/cPanel-PublicAPI - A perl module for interfacing with cPanel's various APIs
• bingos/poe - (perl) portable multitasking and networking framework for Perl (mirror of the svn repository)
• xsawyerx/gitflux - A Perl port of gitflow. Really? Yes, really!
• wehu/CljPerl - CljPerl is a lisp on Perl.
• tomill/Acme-Perlingual - Acme::Perlingual - Convert perl code to php or something.
• TJC/Flickr-API2 - A fork of Flickr::API from Perl's CPAN
• soarpenguin/perl-scripts - useful perl script and snippets of code.
• shogo82148/Redis-Fast - fast perl binding for Redis database
• shlomif/catable - CATAlyst BLog Engine - written by perl cats
• rjbs/Perl-PrereqScanner - scan a set of Perl libraries to figure out prereqs, without loading the code
• reyjrar/DreamCatcher - DNS Monitoring Suite
• petdance/file-next - File::Next, a file finding module for Perl 5
• Perl-Email-Project/Email-Valid - perl library to validate email addresses
• perl6/evalbot - IRC bot for executing Perl 6 code

"The output of the program is Microsoft XL table and publish-ready idiogram picture."

Address of the bookmark: https://compcytogen.pensoft.net/articles.php?id=20830