Open Source Tools

90

Bn

BLAST NCBI 1990

Bn

BLAST NCBI BLAST NCBI About: The Basic Local Alignment Search Tool aka (BLAST) is the most widely used sequence similarity tool. There are versions of BLAST that compare protein queries to protein databases, nucleotide queries to nucleotide databases, as well as versions that translate nucleotide queries or databases in all six frames and compare to protein databases or queries. Year of release: 1990 Download: http://blast.ncbi.nlm.nih.gov/Blast.cgi Author: Stephen Altschul, Warren Gish, Webb Miller, Eugene Myers, and David J. Lipman DOI: 10.1016/S0022-2836(05)80360-2 OS: Windows, Unix, Mac OS X Licence: Public Domain Category: Aligners (pairwise) 08

So

SOAP 2008

So

SOAP SOAP About: SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Year of release: 2008 Download: http://soap.genomics.org.cn/ Author: Prof. T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu DOI: 10.1093/bioinformatics/btn025 OS: Linux, MacOSX Licence: GNU GPL v.3 Category: Aligners (short read) 81

Py

PHYLIP 1981

Py

PHYLIP PHYLIP About: PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Year of release: 1981 No altmetric.com data available. Download: http://evolution.genetics.washington.edu/phylip.html Author: Jerry Shurman, Chistopher Meacham, Mary Kuhner, Jan Yamato, Naruya Saitou and Mark Moehring Key publication: http://nebc.nerc.ac.uk/bioinformatics/docs/phylip.html OS: Linux, Mac OS X and Windows Licence: Open source Category: ToolKits and APIs 00

Em

EMBOSS 2000

Em

EMBOSS EMBOSS About: EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Year of release: 2000 No altmetric.com data available. Download: http://emboss.sourceforge.net/ Author: Tim Carver and Lisa Mullan Key publication: http://www.ncbi.nlm.nih.gov/pubmed/10827456 OS: Linux, Mac OS X, Unix and Windows Licence: GPL and LGPL Category: ToolKits and APIs 00

Bj

BIOJAVA 2000

Bj

BIOJAVA BIOJAVA About: BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It includes objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit. Year of release: 2000 Download: http://biojava.org/wiki/Main_Page Author: Thimas Down, Michael Heuer, David Huen, Matthew Pocock, Mark Schreiber, Richard Holland, Martin Szugat, Keith James, Sylvain Foisy, Andreas Prlic, Dickson S. Guedes, Francois Pepin and Jianjiong Gao DOI: 10.1093/bioinformatics/bts494 OS: Mac OS X, Unix, Windows Licence: LGPL v 2.1 Category: ToolKits and APIs 01

Bc

BIOCONDUCTOR 2001

Bc

BIOCONDUCTOR BIOCONDUCTOR About: Bioconductor is an open source, open development software project to provide tools for the analysis and comprehension of high-throughput genomic data. Year of release: 2001 Download: http://www.bioconductor.org/help/publications/books/bioinformatics-and-computational-biology-solutions/microarrays/ Author: Vince Carey, Marc Carlson, Sean Davis and others. DOI: 10.1186/gb-2004-5-10-r80 OS: Linux, Mac OS X and Windows Licence: Artistic 2.0, GPL2 Category: ToolKits and APIs 10

Bi

Bismark 2010

Bi

Bismark Bismark About: A tool to map bisulfite converted sequence reads and determine cytosine methylation states. Year of release: 2010 Download: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ Author: Felix Krueger DOI: 10.1093/bioinformatics/btr167 OS: Linux, Mac OS X and Windows Licence: GPL v3 or later Category: Other Aligners 03

Ms

SWISS-MODEL 2003

Ms

SWISS-MODEL SWISS-MODEL About: SWISS-MODEL is a fully automated protein structure homology-modeling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide. Year of release: 2003 Download: http://swissmodel.expasy.org/ Author: Manuel Peitsch, et al DOI: 10.1093/bioinformatics/bti770 OS: Web-based Licence: Free, commercial users need to sign an agreement. Category: Structure Modelling

98

Hm

HMMER 1998

Hm

HMMER HMMER About: HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. Year of release: 1998 Download: http://hmmer.janelia.org/ Author: Sean R. Eddy DOI: 10.1093/nar/gkr367 OS: Windows, MacOSX, Linux Licence: GPLv3 Category: Aligners (pairwise) 07

Mq

MAQ 2007

Mq

MAQ MAQ About: Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is previously known as mapass2. Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. It is particularly designed for Illumina-Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI SOLiD data. Year of release: 2007 Download: http://maq.sourceforge.net/ Author: Heng Li DOI: 10.1101/gr.078212.108 OS: Linux Licence: GNU GPL v3 Category: Aligners (short read) 01

Bs

bioSQL 2001

Bs

bioSQL bioSQL About: BioSQL is a generic unifying schema for storing sequences from different sources, for instance Genbank or Swissprot. BioSQL is meant to be a common data storage layer supported by all the different Bio* projects, Bioperl, Biojava, Biopython, and Bioruby. Entries stored through an application written in, say, Bioperl could be retrieved by another written in Biojava. Year of release: 2001 Download: http://www.biosql.org/wiki/Main_Page Author: Ewan Birney DOI: 10.1186/2041-1480-1-8 OS: Unix, Mac OS X, Windows Licence: GNU Lesser General Public Licence v 3 Category: Database/Warehouse 00

Eh

eHIVE 2000

Eh

eHIVE eHIVE About: This is a distributed processing system based on 'autonomous agents' and the behavioural structure of honey bees. It implements all functionality of both data-flow graphs and block-branch diagrams which should allow it to codify any program, algorithm, or parallel processing job control system. It is not bound to any processing 'farm' system and can be adapted to any GRID. Year of release: 2000 Download: http://www.ensembl.org/info/docs/eHive/index.html Author: Abel Ureta-Vidal, Jessica Severin, Michael Schuster DOI: 10.1186/1471-2105-11-240 OS: Linux, Mac OS X, Windows Licence: Open Source Category: Workflows 00

En

ENSEMBL API 2000

En

ENSEMBL API ENSEMBL API About: The Ensembl API (application programming interface) is a framework for applications that need to access or store data in Ensembl's databases. Year of release: 2000 No altmetric.com data available. Download: http://www.ensembl.org/info/docs/api/index.html Author: Glenn Proctor, Ian Longden and Patrick Meidl Key publication: OS: Unix, Windows Licence: Apache-style licence. Category: ToolKits and APIs 00

Br

bioRUBY 2000

Br

bioRUBY bioRUBY About: BioRuby is an open source Ruby library for developing bioinformatics software. Year of release: 2000 Download: http://bioruby.open-bio.org/ Author: Toshiaki Katayama DOI: 10.1093/bioinformatics/btq475 OS: Linux, Mac OS X and Windows Licence: Ruby licence Category: ToolKits and APIs 03

La

LAGAN 2003

La

LAGAN LAGAN About: The LAGAN Tookit consists of four components:CHAOS, LAGAN, Multi-LAGAN,Shuffle-LAGAN. Year of release: 2003 Download: http://lagan.stanford.edu/lagan_web/authors.shtml Author: Michael Brudno DOI: 10.1101/gr.926603 OS: Linux, Windows Licence: GNU GPL Category: ToolKits and APIs 10

Mve

Mauve 2010

Mve

Mauve Mauve About: Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences. Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the amount of sequence being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. Year of release: 2010 Download: http://gel.ahabs.wisc.edu/mauve/ Author: Darling AE, Mau B, Perna NT DOI: 10.1371/journal.pone.0011147 OS: Windows, Mac, Linux Licence: GNU GPL Category: Other Aligners 05

Hh

HHpred 2005

Hh

HHpred HHpred About: The primary aim in developing HHpred was to provide biologists with a method for sequence database searching and structure prediction that is as easy to use as BLAST or PSI-BLAST and that is at the same time much more sensitive in finding remote homologs. In fact, HHpred's sensitivity is competitive with the most powerful servers for structure prediction currently available. Year of release: 2005 Download: http://toolkit.tuebingen.mpg.de/hhpred Author: Soding, Biegert, Lupas, et al DOI: 10.1093/nar/gki408 OS: Linux, Mac OS X Licence: GPL v3 Category: Structure Modelling

99

Mu

MUMmer 1999

Mu

MUMmer MUMmer About: MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. Year of release: 1999 Download: http://mummer.sourceforge.net/ Author: Stefan Kurtz, Adam Phillippy, Art Delcher and Steven Salzberg DOI: 10.1186/gb-2004-5-2-r12 OS: Unix Licence: Artistic License Category: Aligners (pairwise) 08

Bo

Bowtie 2008

Bo

Bowtie Bowtie About: Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. It aligns 35-base-pair reads to the human genome at a rate of 25 million reads per hour on a typical workstation. Year of release: 2008 Download: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Author: Ben Langmead and Cole Trapnell DOI: 10.1038/nmeth.1923 OS: Windows, Linux, MacOSX Licence: GNU GPL v3 Category: Aligners (short read) 94

Cl

CLUSTALW 1994

Cl

CLUSTALW CLUSTALW About: Clustal W is a general purpose multiple alignment program for DNA or proteins. Clustal 2 comes in two flavors: the command-line version ClustalW and the graphical version ClustalX. Year of release: 1994 Download: http://www.clustal.org/clustal2/ Author: Higgins DG, Sharp PM DOI: 10.1093/bioinformatics/btm404 OS: Linux, MacOSX, Windows Licence: GNU Lesser GPL Category: Multiple Sequence Aligners 06

Pe

PECAN 2006

Pe

PECAN PECAN About: Pecan is a consistency based multiple-alignment program developed by Benedict Paten in Ewan Birney's group at the EBI. Year of release: 2006 Download: http://www.ebi.ac.uk/~bjp/pecan/ Author: Benedict Paten DOI: 10.1101/gr.076554.108 OS: Linux Licence: Category: Multiple Sequence Aligners 97

Mi

MIRA 97 1997

Mi

MIRA 97 MIRA 97 About: MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio. It can be seen as a Swiss army knife of sequence assembly developed and used in the past 12 years to get assembly jobs done efficiently - and especially accurately. Year of release: 1997 No altmetric.com data available. Download: http://sourceforge.net/apps/mediawiki/mira-assembler/index.php?title=Main_Page Author: Bastien Chevreux Key publication: http://www.bioinfo.de/isb/gcb99/talks/chevreux/ OS: Linux, Unix Licence: GNU GPL v2 Category: Assemblers Genomic (long read) 04

Se

SEQCLEAN 2004

Se

SEQCLEAN SEQCLEAN About: A script for automated trimming and validation of ESTs or other DNA sequences by screening for various contaminants, low quality and low-complexity sequences. Year of release: 2004 No altmetric.com data available. Download: http://compbio.dfci.harvard.edu/tgi/software/ Author: The Gene Indices Group -Geo Pertea- Key publication: OS: Linux, Windows Licence: Artistic licence Category: Assemblers Genomic (long read) 01

Jm

Jmol 2001

Jm

Jmol Jmol About: Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. Year of release: 2001 No altmetric.com data available. Download: http://jmol.sourceforge.net/ Author: Egon Willighagen, et al Key publication: http://www.scribd.com/doc/14333194/Processing-CML-Conventions-in-Java OS: Linux, Windows, Mac OS X Licence: LGPL Category: Structure Visualisation 09

Sd

SOAP: DE NOVO 2 2009

Sd

SOAP: DE NOVO 2 SOAP: DE NOVO 2 About: SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. Year of release: 2009 Download: http://soap.genomics.org.cn/soapdenovo.html Author: BGI DOI: 10.1186/2047-217X-1-18 OS: Linux, Mac OS X Licence: GPLv3 Category: Assemblers Genomic (short read) 03

Un

UNIGENE 2003

Un

UNIGENE UNIGENE About: UniGene computationally identifies transcripts from the same locus; analyzes expression by tissue, age, and health status; and reports related proteins (protEST) and clone resources. Year of release: 2003 No altmetric.com data available. Download: http://www.ncbi.nlm.nih.gov/unigene/ Author: Boguski MS, Schuler GD Key publication: http://www.ncbi.nlm.nih.gov/books/NBK21083/ OS: Linux, Mac OS X, Windows Licence: Open licence Category: Assemblers (mRNA) 98

Gl

GLIMMER 3 1998

Gl

GLIMMER 3 GLIMMER 3 About: Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Year of release: 1998 Download: http://www.cbcb.umd.edu/software/glimmer/ Author: Arthur Delcher DOI: 10.1093/bioinformatics/btm009 OS: Linux Licence: OSI Certified Open source Category: Gene Prediction (mRNA) 06

Cd

CD-HIT 2006

Cd

CD-HIT CD-HIT About: CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. Year of release: 2006 Download: http://weizhong-lab.ucsd.edu/cd-hit/ Author: Wizhong Li, Adam Godzik, Lukasz Jaroszewski DOI: 10.1093/bioinformatics/btl158 OS: Linux Licence: GPL v2 Category: Sequence Tools 97

Tr

tRNAscan 1997

Tr

tRNAscan tRNAscan About: tRNAscan-SE was designed to make rapid, sensitive searches of genomic sequence feasible using the selectivity of the Cove analysis package. Search for tRNA genes in genomic sequence.tRNAscan-SE identifies transfer RNA genes in genomic DNA or RNA sequences. Year of release: 1997 No altmetric.com data available. Download: http://lowelab.ucsc.edu/tRNAscan-SE/ Author: Oeter Schattner, Angela N. Brooks and Todd M. Lowe Key publication: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/ OS: Unix Licence: GNU GPL Category: Gene Prediction (ncRNA) 03

Bm

bioMART 2003

Bm

bioMART bioMART About: The purpose of BioMart is to convert one or more data source (flat files or relational) into data marts which can be accessed via its tandardised web browser interface and also via its Perl, Java and webservice APIs. Year of release: 2003 Download: http://www.biomart.org/ Author: Arek Kasprzyk DOI: 10.1093/database/bar038 OS: Linux Licence: Open Source Category: Database/Warehouse 03

Ta

TAVERNA 2003

Ta

TAVERNA TAVERNA About: Taverna is an open source and domain-independent Workflow Management System – a suite of tools used to design and execute scientific workflows and aid in silico experimentation. Year of release: 2003 Download: http://www.taverna.org.uk/ Author: myGrid (University of Manchester) and EBI) DOI: 10.1093/nar/gkt328 OS: Linux, Mac OS X, Windows Licence: LPGL Category: Workflows 00

Eb

ENSEMBL BROWSER 2000

Eb

ENSEMBL BROWSER ENSEMBL BROWSER About: Ensembl is a joint project between EMBL - EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Year of release: 2000 Download: http://www.ensembl.org/index.html Author: EBI and Wellcome Trust Sanger Institute DOI: 10.1101/gr.1863004 OS: Linux Licence: Apache-style licence. Category: Genome Browsers 00

Bp

bioPERL 2000

Bp

bioPERL bioPERL About: BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. BioPerl project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research. Year of release: 2000 Download: http://www.bioperl.org/wiki/Main_Page Author: Chris Dagdigian, Richard Resnick, Lew Gramer,Alessandro Guffanti and others. DOI: 10.1101/gr.361602 OS: Linux, Mac OS X, Windows Licence: Perl Artistic Licence Category: ToolKits and APIs 07

Pl

PLINK 2007

Pl

PLINK PLINK About: PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Year of release: 2007 No altmetric.com data available. Download: http://pngu.mgh.harvard.edu/~purcell/plink/ Author: Shaun Purcell Key publication: http://pngu.mgh.harvard.edu/purcell/plink/ OS: Linux, Mac OS X Licence: GNU v.2 Category: ToolKits and APIs 09

Sa

SAMtools 2009

Sa

SAMtools SAMtools About: SAMtools is a set of utilities for efficiently processing nucleotide alignments in the Sequence Alignment/Map format (SAM) and its binary representation (BAM format), and accurately calling the SNPs and short INDELs from the alignment. Year of release: 2009 Download: http://samtools.sourceforge.net/ Author: Heng Li,Bob Handsaker, Jue Ruan, John Marshall and Petr Danecek DOI: 10.1093/bioinformatics/btp352 OS: Linux Licence: BSD licence, MIT Licence Category: ToolKits and APIs 99

Ps

PSIPRED 1999

Ps

PSIPRED PSIPRED About: The PSIPRED Protein Sequence Analysis Workbench aggregates several UCL structure prediction methods into one location. Users can submit a protein sequence, perform the predictions of their choice and receive the results of the prediction via e-mail or the web. Year of release: 1999 Download: http://bioinf.cs.ucl.ac.uk/psipred/ Author: Jones, Buchan, Nugent, Minneci, Bryson et al DOI: 10.1093/nar/gkq427 OS: Web-based, Linux Licence: Custom free licence Category: Structure Modelling

03

Ss

SSAHA 2003

Ss

SSAHA SSAHA About: ssaha is a tool for rapidly finding near exact matches in DNA or protein databases. The name is an acronym standing for Sequence Search and Alignment by Hashing Algorithm. It works by converting a sequence database into a hash table. This is then rapidly quizzed for hits, which are concatenated into matches. Year of release: 2003 Download: http://www.sanger.ac.uk/resources/software/ssaha/ Author: Prof. T.W. Lam, Alan Tam, Simon Wong, Edward Wu and S.M. Yiu DOI: 10.1101/gr.194201 OS: Linux Licence: GNU GPL v2 Category: Aligners (pairwise) 09

Bw

BWA 2009

Bw

BWA BWA About: Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. It implements two algorithms, bwa-short and BWA-SW. Year of release: 2009 Download: http://bio-bwa.sourceforge.net/ Author: Heng Li, Chi-Kwong, Nong Ge and Yuta Mori. DOI: 10.1093/bioinformatics/btp324 OS: Licence: GPLv3 Category: Aligners (short read) 00

Cf

T-COFFEE 2000

Cf

T-COFFEE T-COFFEE About: T-Coffee is a multiple sequence alignment package. You can use T-Coffee to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment. Year of release: 2000 Download: http://tcoffee.org/ Author: Cedric Notredame, Higgins DG, Heringa J. DOI: 10.1006/jmbi.2000.4042 OS: Unix, Linux, MacOSX, Windows Licence: GNU GPLv3 Category: Multiple Sequence Aligners 10

Pr

PRANK 2010

Pr

PRANK PRANK About: PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences that has been shown to produce exceptionally accurate alignments for evolutionary analyses. It is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. Year of release: 2010 Download: http://www.ebi.ac.uk/goldman-srv/prank/ Author: Ari Löytynoja DOI: 10.1186/1471-2105-11-579 OS: Licence: GPL Category: Multiple Sequence Aligners 97

Ce

CELERA 1997

Ce

CELERA CELERA About: Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. Year of release: 1997 Download: http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page Author: Celera Gomes DOI: 10.1126/science.287.5461.2196 OS: Linux, Mac OS X, Unix Licence: GNU GPL/ BSD Category: Assemblers Genomic (long read) 09

Fo

FORGE 2009

Fo

FORGE FORGE About: Forge is a classic Overlap layout consensus genome assembler. Implemented in C++ and using the parallel MPI library, it runs on one or more machines in a network and can scale to very large numbers of reads provided there is enough collective memory on the machines used. Year of release: 2009 Download: http://combiol.org/forge/ Author: Darren Platt and Dirk Evers DOI: 10.1186/gb-2009-10-9-r94 OS: Unix Licence: Licenced under Apache 2.0 licence Category: Assemblers Genomic (long read) 95

Rm

RasMol 1995

Rm

RasMol RasMol About: RasMol is an important scientific tool for visualisation of molecules created by Roger Sayle in 1992. RasMol is used by hundreds of thousands of users world-wide to view macromolecules and to prepare publication-quality images. Year of release: 1995 Download: http://rasmol.org/ Author: R. A. Sayle and E. J. Milner-White DOI: 10.1016/S0968-0004(00)89080-5 OS: Universal Licence: GPL Category: Structure Visualisation 09

Sg

SGA 2009

Sg

SGA SGA About: SGA is a de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. Year of release: 2009 Download: https://github.com/jts/sga Author: Jared Simpson and Richard Durbin DOI: 10.1101/gr.126953.111 OS: Linux Licence: GNU GPL v3 Category: Assemblers Genomic (short read) 09

Cu

CUFFLINKS 2009

Cu

CUFFLINKS CUFFLINKS About: Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. Year of release: 2009 Download: http://cufflinks.cbcb.umd.edu/ Author: Cole Trapnell, Adam Roberts, Ali Mortazavi, Steven Salzberg, Barabara Wold, Lior Pachter etc. DOI: 10.1038/nbt.1621 OS: Linux, Mac OS X Licence: OSI-approved Boost Licence Category: Assemblers (mRNA) 99

Eu

EUGENE 1999

Eu

EUGENE EUGENE About: An open gene finder for eukaryotic organisms. Compared to most existing gene finders, EuGène is characterized by its ability to simply integrate arbitrary sources of information in its prediction process. Year of release: 1999 Download: http://eugene.toulouse.inra.fr/ Author: P. Bardou, MJ. Cros, S. Foissac, J Gouzy, A. and Moisan, T. Schiex DOI: 10.1007/3-540-45727-5_10 OS: Linux Licence: Artistic licence Category: Gene Prediction (mRNA) 09

Fx

FASTX-Toolkit 2009

Fx

FASTX-Toolkit FASTX-Toolkit About: The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. Year of release: 2009 Download: http://hannonlab.cshl.edu/fastx_toolkit/ Author: Assaf Gordon DOI: 10.1006/geno.1997.4995 OS: Linux, Unix Licence: GNU Affero Category: Sequence Tools 10

Rn

RNAfold 2010

Rn

RNAfold RNAfold About: The RNAfold web server will predict secondary structures of single stranded RNA or DNA sequences. Year of release: 2010 No altmetric.com data available. Download: http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi Author: M Zuker and P Stiegler Key publication: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC326673/ OS: Linux, Mac OS X and Windows Licence: Open Source Category: Gene Prediction (ncRNA) 07

In

INTERMINE 2007

In

INTERMINE INTERMINE About: InterMine is a powerful open source data warehouse system. Using InterMine, you can create databases of biological data accessed by sophisticated web query tools. InterMine includes an attractive, user-friendly web interface that works 'out of the box' and can be easily customised for your specific needs. Year of release: 2007 Download: http://intermine.org/wiki/InterMineOverview?redirectedfrom=InterMine Author: Richard Smith, Jakub Kulaviak, Julie Sullivan, Mather Wakeling, Xavier Watkins DOI: 10.1093/database/bar062 OS: Linux Licence: GNU Lesser General Public Licence Category: Database/Warehouse 07

Gx

GALAXY 2007

Gx

GALAXY GALAXY About: Galaxy is a scientific workflow and data integration platform that aims to make computational biology accessible to research scientists that do not have computer programming experience. Year of release: 2007 Download: http://wiki.g2.bx.psu.edu/FrontPage Author: Enis Afgan, Guru Ananda and Dannon Baker DOI: 10.1186/gb-2010-11-8-r86 OS: Unix Licence: GNU Category: Workflows 02

Ap

APOLLO 2002

Ap

APOLLO APOLLO About: Apollo is a genome annotation viewer and editor. It was developed as a collaboration between the Berkeley Drosophila Genome Project (part of the FlyBase consortium) and The Sanger Institute in Cambridge, UK. Apollo allows researchers to explore genomic annotations at many levels of detail, and to perform expert annotation curation, all in a graphical environment. Year of release: 2002 Download: http://apollo.berkeleybop.org/current/index.html Author: Ed Lee, Nomi Harris, Steve Searle, Michele Clamp, Suzanna Lewis, John Richter and Mark Gibson DOI: 10.1186/gb-2002-3-12-research0082 OS: Linux, MacOsX, Unix and Windows Licence: Artistic Licence Category: Genome Browsers 04

Ig

IGB 2004

Ig

IGB IGB About: The Integrated Genome Browser (IGB, pronounced Ig-Bee) is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets. Year of release: 2004 Download: http://bioviz.org/igb/ Author: Gregg Helt DOI: 10.1093/bioinformatics/btp472 OS: Linux, MacOSX, Unix and Windows Licence: Common Public Licence v 1.0 Category: Genome Browsers 07

Ut

UTGB 2007

Ut

UTGB UTGB About: UTGB Toolkit is an open-source software for developing personalized genome browsers. Year of release: 2007 Download: http://utgenome.org/ Author: Shinichi Morishita, Taro Saito, Jun Yoshimura, Koichiro Higasa, Hiroshi Minoshima, Reginaldo Kuroshu and Atsushi Sasaki. DOI: 10.1093/bioinformatics/btp350 OS: Linux, Mac OS X and Windows Licence: Apache Licence 2.0 Category: ToolKits and APIs 10

Am

AMPLICONNOISE 2010

Am

AMPLICONNOISE AMPLICONNOISE About: AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal. Year of release: 2010 Download: http://code.google.com/p/ampliconnoise/ Author: Chrisopher Quince, Andres Lanzen, Russell J Davenport DOI: 10.1186/1471-2105-12-38 OS: Linux and Mac OS X Licence: GNU Lesser GPL Category: ToolKits and APIs 09

Qi

QIIME 2009

Qi

QIIME QIIME About: QIIME (canonically pronounced ‘Chime’) is a pipeline for performing microbial community analysis that integrates many third party tools which have become standard in the field. QIIME can run on a laptop, a supercomputer, and systems in between such as multicore desktops. Year of release: 2009 Download: http://www.qiime.org/ Author: Developed by Knight Lab at the University of Colorado at Boulder DOI: 10.1038/nmeth.f.303 OS: Linux, MacOSX and Windows Licence: Category: ToolKits and APIs

05

Ex

EXONERATE 2005

Ex

EXONERATE EXONERATE About: exonerate is a general tool for sequence comparison. It uses the C4 dynamic programming library. It is designed to be both general and fast. It can produce either gapped or ungapped alignments, according to a variety of different alignment models. Year of release: 2005 Download: http://www.ebi.ac.uk/~guy/exonerate/ Author: Guy St.C. Slater DOI: 10.1186/1471-2105-6-31 OS: UNIX, Linux Licence: GNU GPL 2005 Category: Aligners (pairwise) 09

Bf

BFAST 2009

Bf

BFAST BFAST About: BFAST (Blat-like Fast Accurate Search Tool) facilitates the fast and accurate mapping of short reads to reference sequences. BFAST was designed to facilitate whole-genome resequencing, where mapping billions of short reads with variants is of utmost importance. BFAST supports both Illumina and ABI SOLiD data, as well as any other Next-Generation Sequencing Technology (454, Helicos), with particular emphasis on sensitivity towards errors, SNPs and especially indels. Year of release: 2009 Download: http://bfast.sf.net/ Author: Nils Homer DOI: 10.1371/journal.pone.0007767 OS: Unix, Linux, MacOSX Licence: GPL v2 Category: Aligners (short read) 02

Ma

MAFFT 2002

Ma

MAFFT MAFFT About: MAFFT is a multiple sequence alignment program for amino acid or nucleotide sequences. It has several different options for various types of alignment problems. Progressive alignment options can be applied to a large number of homologous sequences. Year of release: 2002 Download: http://mafft.cbrc.jp/alignment/server/ Author: Kazutaka Katoh, Charles Plessy DOI: 10.1093/bioinformatics/btq224 OS: Linux, MacOSX, Windows Licence: GPL and BSD Category: Multiple Sequence Aligners 04

Mv

MAVID 2004

Mv

MAVID MAVID About: MAVID is a multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences. The sequences can be small mitochondrial genomes or large genomic regions up to megabases long. Year of release: 2004 Download: http://bio.math.berkeley.edu/mavid/download/ Author: Nicolas Bray, Lior Pachter DOI: 10.1101/gr.1960404 OS: Unix, Linux, MacOSX Licence: Open Source Category: Multiple Sequence Aligners 02

Ar

ARACHNE 2002

Ar

ARACHNE ARACHNE About: ARACHNE is a program for assembling data from whole genome shotgun sequencing experiments. It was designed for long reads from Sanger sequencing technology, and has been used extensively to assemble many genomes, including many that are large and highly repetitive. Year of release: 2002 Download: http://www.broadinstitute.org/crd/wiki/index.php/Arachne_Main_Page Author: Jaffe DB DOI: 10.1101/gr.208902 OS: Linux Licence: Category: Assemblers Genomic (long read) 10

Me

MERACULOUS 2010

Me

MERACULOUS MERACULOUS About: Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. Year of release: 2010 Download: ftp://ftp.jgi-psf.org/pub/JGI_data/meraculous/Meraculous-1.4.4-rel.tar Author: Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP DOI: 10.1371/journal.pone.0023501 OS: Unix Licence: GNU GPL Category: Assemblers Genomic (long read) 08

Co

CORTEX_CON_RP 2008

Co

CORTEX_CON_RP CORTEX_CON_RP About: Cortex is an efficient and low-memory software framework for analysis of genomes using sequence data. Year of release: 2008 Download: http://cortexassembler.sourceforge.net/index.html Author: Mario Caccamo and Zamin Iqbal DOI: 10.1038/ng.1028 OS: Linux, Mac OS X Licence: GPLv3 Category: Assemblers Genomic (short read) 10

Pa

PE-ASSEMBLER 2010

Pa

PE-ASSEMBLER PE-ASSEMBLER About: A simple extension approach to assembling paired-end reads and capable of parallelization. Year of release: 2010 Download: http://www.comp.nus.edu.sg/~bioinfo/peasm/PE_manual.htm Author: Nuwantha Ariaratne P., Sung WK. DOI: 10.1093/bioinformatics/btq626 OS: Linux Licence: Open Source Category: Assemblers Genomic (short read) 10

Oa

OASES 2010

Oa

OASES OASES About: Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. Year of release: 2010 Download: http://www.ebi.ac.uk/~zerbino/oases/ Author: Marcel Schulz and Daniel Zerbino DOI: 10.1093/bioinformatics/bts094 OS: Linux Licence: GPL Category: Assemblers (mRNA) 00

Ep

ENSEMBL PIPELINE 2000

Ep

ENSEMBL PIPELINE ENSEMBL PIPELINE About: Ensembl is a joint project between EMBL - EBI and the Wellcome Trust Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes. Year of release: 2000 Download: http://www.ensembl.org/info/docs/Doxygen/pipeline-api/files.html Author: EBI and Wellcome Trust Sanger institute. DOI: 10.1093/nar/gkq1064 OS: Linux, Mac OS X, Windows Licence: Apache-style licence. Category: Gene Prediction (mRNA) 10

Fq

FastQC 2010

Fq

FastQC FastQC About: A quality control tool for high throughput sequence data. Year of release: 2010 No altmetric.com data available. Download: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Author: Simon Andrews Key publication: OS: Linux, Mac OS X, Windows Licence: GPL v3 or later Category: Sequence Tools 12

St

Strelka 2012

St

Strelka Strelka About: Strelka is an analysis package designed to detect somatic SNVs and small indels from the aligned sequencing reads of matched tumor-normal samples. Year of release: 2012 Download: https://sites.google.com/site/strelkasomaticvariantcaller/ Author: Christopher T. Saunders; Wendy Wong; Sajani Swamy; Jennifer Becq; Lisa J. Murray; R. Keira Cheetham DOI: 10.1093/bioinformatics/bts271 OS: Linux Licence: Free Category: Sequence Tools 10

Ch

CHADO 2010

Ch

CHADO CHADO About: Chado is a relational database schema that underlies many GMOD installations. The Chado schema has been designed with modularity and compartmentalization of function in mind. Year of release: 2010 Download: http://gmod.org/wiki/Chado Author: Chris Mungall and Dave Emmert DOI: 10.1093/database/bar051 OS: Unix, Windows Licence: Artistic Licence Category: Database/Warehouse 08

Kn

KNIME 2008

Kn

KNIME KNIME About: KNIME (Konstanz Information Miner) is a user-friendly and comprehensive open-source data integration, processing, analysis, and exploration platform. Year of release: 2008 Download: http://www.knime.org/ Author: Iris Ada, Michael Berhold and Thomas Gabriel DOI: 10.1093/bioinformatics/btr478 OS: Linux, Mac OS X, Windows Licence: GNU GPL v.3 Category: Workflows 02

Gb

GBROWSE 2002

Gb

GBROWSE GBROWSE About: GBrowse is a combination of database and interactive web pages for manipulating and displaying annotations on genomes. Year of release: 2002 Download: http://gmod.org/wiki/Gbrowse Author: Lincoln Stein DOI: 10.1101/gr.403602 OS: Linux, MacOSX and Windows Licence: Perl Artistic Licence Category: Genome Browsers 04

Nc

NCBI MapViewer 2004

Nc

NCBI MapViewer NCBI MapViewer About: The Map Viewer provides special browsing capabilities for a subset of organisms in Entrez Genomes. The viewer allows you to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. Year of release: 2004 Download: http://www.ncbi.nlm.nih.gov/mapview/static/MapViewerHelp.html#Overview Author: DOI: 10.1002/0471250953.bi0105s16 OS: Mac OS X, Unix and Windows Licence: Category: Genome Browsers 03

By

BioPython 2003

By

BioPython BioPython About: Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. Year of release: 2003 Download: http://biopython.org/wiki/Biopython Author: Tiago Antao, Sebastian Bassi, Jeffrey Chang etc. DOI: 10.1093/bioinformatics/btp163 OS: MacOsx, Unix and Windows Licence: Biopython License Category: ToolKits and APIs 09

Pic

Picard 2009

Pic

Picard Picard About: Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported. Year of release: 2009 No altmetric.com data available. Download: http://picard.sourceforge.net/ Author: Key publication: http://picard.sourceforge.net/ OS: Licence: Apache License V2.0, MIT License Category: ToolKits and APIs 09

Vc

VCFtools 2009

Vc

VCFtools VCFtools About: Welcome to VCFtools - a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. VCFtools is split into two sections: The vcftool binary program/ The VCF perl module. Year of release: 2009 Download: http://vcftools.sourceforge.net/ Author: Adam Auton and Petr Danecek DOI: 10.1093/bioinformatics/btr330 OS: Linux and Mac OS X Licence: GNU General Public Licence version 3.0 Category: ToolKits and APIs

88

Fa

FASTA 1988

Fa

FASTA FASTA About: FASTA is a DNA and protein sequence alignment software package first described (as FASTP). Its legacy is the FASTA format which is now ubiquitous in bioinformatics. FASTA is pronounced 'fast A', and stands for 'FAST-All', because it works with any alphabet, an extension of 'FAST-P' (protein) and 'FAST-N' (nucleotide) alignment. Year of release: 1988 No altmetric.com data available. Download: http://en.wikipedia.org/wiki/FASTA Author: David Lipman and William Pearson Key publication: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC280013/?tool=pmcentrez OS: Unix, Linux, MacOSX, Windows Licence: Free for academic users. Category: Aligners (pairwise) 10

Sm

SMALT 2010

Sm

SMALT SMALT About: SMALT efficiently aligns DNA sequencing reads with genomic reference sequences. The software employs a perfect hash index of short words (< 21 nucleotides long), sampled at equidistant steps along the genomic reference sequences. For each read, potentially matching segments in the reference are identified from seed matches in the index and subsequently aligned with the read using a banded Smith-Waterman algorithm. Reads from a wide range of sequencing platforms, for example Illumina, Roche-454, Ion Torrent, PacBio or ABI-Sanger, can be processed including paired-end reads. Year of release: 2010 No altmetric.com data available. Download: http://www.sanger.ac.uk/resources/software/smalt/ Author: Hannes Ponstigl Key publication: OS: Unix Licence: GNU GPL Category: Aligners (short read) 12

Rs

rna-star 2012

Rs

rna-star rna-star About: To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. Year of release: 2012 Download: https://code.google.com/p/rna-star/ Author: Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson and Thomas R. Gingeras DOI: 10.1093/bioinformatics/bts635 OS: Universal Licence: GPL v3 Category: Aligners (short read) 05

Pb

PROBCONS 2005

Pb

PROBCONS PROBCONS About: ProbCons is an open source probabilistic consistency-based multiple alignment of amino acid sequences. It is an efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools. Year of release: 2005 Download: http://probcons.stanford.edu/about.html Author: Chuong Do, Michael Brudno DOI: 10.1101/gr.2821705 OS: Unix Licence: Open Source Category: Multiple Sequence Aligners 03

Ph

PHUSION(2) 2003

Ph

PHUSION(2) PHUSION(2) About: Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads. The Phusion assembler is involved in assembling a number of genomes, such as mouse, zebrafish, C. briggsae, Schistosoma mansoni etc. Year of release: 2003 Download: http://www.sanger.ac.uk/resources/software/phusion/ Author: Mullikin JC and Zemin Ning DOI: 10.1101/gr.731003 OS: Unix Licence: Creative Commons Attribution 3.0 Unported Licence Category: Assemblers Genomic (long read) 10

Qu

QUAKE 2010

Qu

QUAKE QUAKE About: Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads. Quake adopts the k-mer error correction framework, first introduced by the EULER genome assembly package. Year of release: 2010 Download: http://www.cbcb.umd.edu/software/quake/ Author: David R. Kelly, Michael C. Schatz, Steven L. Salzberg DOI: 10.1186/gb-2010-11-11-r116 OS: Linux Licence: Pearl Artistic Licence Category: Assemblers Genomic (long read) 07

Al

ALLPATHS-LG 2007

Al

ALLPATHS-LG ALLPATHS-LG About: ALLPATHS LG is a whole-genome shotgun assembler that can generate high-quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. The significant difference between ALLPATHS and traditional assemblers such as Arachne is that ALLPATHS assemblies are not necessarily linear, but instead are presented in the form of a graph. Year of release: 2007 Download: http://www.broadinstitute.org/science/programs/genome-biology/crd Author: Gnerre S. DOI: 10.1101/gr.7337908 OS: Linux, Unix Licence: Open Source Licence Category: Assemblers Genomic (short read) 09

Ba

BAMBUS 2 09 2009

Ba

BAMBUS 2 09 BAMBUS 2 09 About: Bambus 2.0, the second generation Bambus scaffolder for polymorphic and metagenomic data. Year of release: 2009 Download: http://www.cbcb.umd.edu/software/bambus/ Author: Segey Koren and Mihai Pop DOI: 10.1101/gr.1536204 OS: Linux Licence: Open source Category: Assemblers Genomic (short read) 11

Ty

Trinity 2011

Ty

Trinity Trinity About: Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Year of release: 2011 Download: http://trinityrnaseq.sourceforge.net/ Author: Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. DOI: 10.1038/nbt.1883 OS: Linux Licence: BSD Category: Assemblers (mRNA) 11

Sn

SNAP 2011

Sn

SNAP SNAP About: The SNAP gene finder is HMM-based like Genscan and attempts to be more adaptable to different organisms, addressing problems related to using a gene finder on a genome sequence that it was not trained against. Year of release: 2011 Download: http://korflab.ucdavis.edu/software.html Author: Ian Korf DOI: 10.1186/1471-2105-5-59 OS: Linux Licence: GNU GPL Category: Gene Prediction (mRNA) 96

Rk

RepeatMasker 1996

Rk

RepeatMasker RepeatMasker About: RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher. Year of release: 1996 Download: http://www.repeatmasker.org/ Author: Smit, AFA, Hubley, R, Green, P. DOI: 10.1002/0471250953.bi0410s05 OS: Universal Licence: OSL v2.1 Category: Sequence Tools 11

Vt

VariantTools 2011

Vt

VariantTools VariantTools About: Variant tools is a software tool for the annotation, selection, and analysis of variants in the context of next-gen sequencing analysis. Unlike some other tools used for Next-Gen sequencing analysis, variant tools is project based and provide a whole set of tools to manipulate and analyze genetic variants. Year of release: 2011 Download: http://varianttools.sourceforge.net/ Author: F Anthony San Lucas, Gao Wang, Paul Scheet, Bo Peng DOI: 10.1093/bioinformatics/btr667 OS: Mac, Linux Licence: GPL v3 Category: Sequence Tools 71

Pd

PDB 1971

Pd

PDB PDB About: The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome. Year of release: 1971 Download: http://www.rcsb.org/pdb Author: Consortium. DOI: 10.1093/nar/28.1.235 OS: Linux, Mac OS X and Windows Licence: Data contained in PDF is free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use. Category: Database/Warehouse 03

Up

UniProt 2003

Up

UniProt UniProt About: The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. Year of release: 2003 Download: http://www.uniprot.org/ Author: Consortium led by Rolf Apweiler, Cathy Wu, and Ioannis Xenarios. DOI: 10.1093/nar/gkr981 OS: Linux, Mac OS X and Windows Licence: Creative Commons Attribution-NoDerivs Category: Database/Warehouse 08

Iv

IGV 2008

Iv

IGV IGV About: The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations. Year of release: 2008 Download: http://www.broadinstitute.org/igv/home Author: Jim Robinson, Helga Thorvaldsdottir, Jacob Silterra and Marc-Danie Nazaire. DOI: 10.1038/nbt.1754 OS: Linux, Mac OS X and Windows Licence: GNU Lesser General Public Licence Category: Genome Browsers 07

Ag

ARGO 2007

Ag

ARGO ARGO About: The Argo Genome Browser is the Broad Institute's production tool for visualizing and manually annotating whole genomes. Year of release: 2007 Download: http://www.broadinstitute.org/annotation/argo/ Author: Reinhard Engels DOI: 10.1093/bioinformatics/btl193 OS: Mac OS X and Windows Licence: GNU General Public Licence Category: Genome Browsers 02

At

ARTEMIS 2002

At

ARTEMIS ARTEMIS About: Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Year of release: 2002 Download: http://www.sanger.ac.uk/resources/software/artemis/ Author: Tim Carver, Giles Velarde, Matthew Berriman, Julian Parkhill and Jacqueline McQuillan. DOI: 10.1093/bioinformatics/16.10.944 OS: Linux, Mac OS X, Unix and Windows. Licence: GNU General Public Licence v. 2.0 Category: Genome Browsers 05

As

APSampler 2005

As

APSampler APSampler About: APSampler is a tool that allows multi-locus and multi-level association analysis of genotypic and phenotypic data. The goal is to find the allelic sets (patterns) that are associated with phenotype. Year of release: 2005 Download: http://code.google.com/p/apsampler/ Author: Dmitrijs Lvov and A.V. Favorov DOI: 10.1534/genetics.105.048090 OS: Linux and Windows Licence: MIT License Category: ToolKits and APIs 12

Ge

GenABEL 2012

Ge

GenABEL GenABEL About: The mission of the GenABEL project is to provide a free framework for collaborative, robust, transparent, open-source based development of statistical genomics methodology. Year of release: 2012 Download: http://www.genabel.org/ Author: GenABEL project developers DOI: 10.1093/bioinformatics/btm108 OS: Linux Licence: GPL v2 Category: ToolKits and APIs

05

Ac

ACT 2005

Ac

ACT ACT About: ACT is a free tool for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. Year of release: 2005 Download: http://www.sanger.ac.uk/resources/software/act/ Author: Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG and Parkhill J DOI: 10.1093/bioinformatics/bti553 OS: Universal Licence: GNU GPL Category: Aligners (pairwise) 10

Ja

JAligner 2010

Ja

JAligner JAligner About: An open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment using the affine gap penalty model. Year of release: 2010 No altmetric.com data available. Download: http://jaligner.sourceforge.net/ Author: Ahmed Moustafa Key publication: OS: Mac OS X, Unix, Windows Licence: GPL Category: Aligners (pairwise) 11

Gm

GMAP/GSNAP 2011

Gm

GMAP/GSNAP GMAP/GSNAP About: GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program Year of release: 2011 Download: http://research-pub.gene.com/gmap/ Author: Thomas D. Wu, Colin K. Watanabe, Serban Nacu DOI: 10.1093/bioinformatics/bti310 OS: Unix, Linux Licence: Free (custom Genentech) but do not redistribute modifications Category: Aligners (short read) 08

Fs

FSA 2008

Fs

FSA FSA About: FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Year of release: 2008 Download: http://fsa.sourceforge.net/ Author: Robert Bradley, Colin Dewey, Jaeyoung Do, Sudeep Juvekar, Lior Pachter, Adam Roberts, and Michael Smoot. DOI: 10.1371/journal.pcbi.1000392 OS: Linux and Mac OS X Licence: GNU GPL Category: Multiple Sequence Aligners 11

Pi

PRICE 2011

Pi

PRICE PRICE About: We are pleased to release PRICE (Paired-Read Iterative Contig Extension), a de novo genome assembler implemented in C++. Its name describes the strategy that it implements for genome assembly: PRICE uses paired-read information to iteratively increase the size of existing contigs. Initially, those contigs can be individual reads from a subset of the paired-read dataset, non-paired reads from sequencing technologies that provide non-paired data, or contigs that were output from a prior run of PRICE or any other assembler. Year of release: 2011 Download: http://derisilab.ucsf.edu/software/price/index.html Author: DOI: 10.1534/g3.113.005967 OS: Linux, MacOS Licence: Open Source Category: Assemblers Genomic (long read) 07

Ve

VELVET 2007

Ve

VELVET VELVET About: Velvet is short read assembler which uses de Bruijn graphs to assemble next-generation sequencing reads into useable contigs. It handles mixed length reads as well as paired-end reads. Year of release: 2007 Download: http://www.ebi.ac.uk/~zerbino/velvet/ Author: Daniel Zerbino and Ewan Birney DOI: 10.1101/gr.074492.107 OS: Linux, Mac OS X Licence: GPL v2.0 Category: Assemblers Genomic (short read) 12

Sp

SPAdes 2012

Sp

SPAdes SPAdes About: SPAdes stands for St. Petersburg genome assembler. It is intended for both standard (multicell) and single-cell MDA bacteria assemblies. Year of release: 2012 Download: http://bioinf.spbau.ru/en/spades Author: Anton Bankevich, Sergey Nurk, Dmitry Antipov etc.'c DOI: 10.1089/cmb.2012.0021 OS: Linux Licence: GPLv2 Category: Assemblers Genomic (short read) 09

Cn

Contrail 2009

Cn

Contrail Contrail About: Similar to other leading short read assembler, Contrail relies on the graph-theoretic framework of de Bruijn graphs. However, unlike these programs, which require large RAM resources, Contrail relies on Hadoop to iteratively transform an on-disk representation of the assembly graph, allowing an in depth analysis even for large genomes. Year of release: 2009 No altmetric.com data available. Download: http://contrail-bio.sf.net/ Author: Michael Schatz, Jeremy Chambers, Avijit Gupta, Rushil Gupta, David Kelley, Jeremy Lewi, Deepak Nettem, Dan Sommer, and Mihai Pop Key publication: OS: All Licence: Unknown Category: Assemblers Genomic (short read) 09

Au

AUGUSTUS 2009

Au

AUGUSTUS AUGUSTUS About: AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. It can be run on this web server, on a new web server for larger input files or be downloaded and run locally. Year of release: 2009 Download: http://augustus.gobics.de/ Author: Mario Stanke and Oliver Keller DOI: 10.1093/bioinformatics/btn013 OS: Linux Licence: Artistic licence 2 Category: Gene Prediction (mRNA) 08

Mg

MGENE 2008

Mg

MGENE MGENE About: mGene is a computational tool for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. Year of release: 2008 Download: http://www.mgene.org/ Author: Gunnar Raetsch, Gabriele Schweikert, Jonas Behr DOI: 10.1101/gr.090597.108 OS: Linux Licence: Open Source Category: Gene Prediction (mRNA) 09

Mm

MetaBioME 2009

Mm

MetaBioME MetaBioME About: MetaBioME is a web resource to find novel homologs for known Commercially Useful Enzymes (CUEs) in metagenomic datasets and completed bacterial genomes. Year of release: 2009 Download: http://metasystems.riken.jp/metabiome/ Author: Vineet Kumar Sharma, Naveen Kumar, Tulika Prakash, Todd D. Taylor DOI: 10.1093/nar/gkp1001 OS: Online Licence: Free to use Category: Sequence Tools 04

Jv

JalView 2004

Jv

JalView JalView About: Jalview is a free program developed for the interactive editing, analysis and visualization of multiple sequence alignments. It can also work with sequence annotation, secondary structure information, phylogenetic trees and 3D molecular structures. Year of release: 2004 Download: http://www.jalview.org/ Author: Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ DOI: 10.1093/bioinformatics/btp033 OS: All Licence: GPL3 Category: Sequence Tools 97

Ct

CATH 1997

Ct

CATH CATH About: The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. Year of release: 1997 Download: http://www.cathdb.info/ Author: Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA DOI: 10.1093/nar/gks1211 OS: Universal Licence: Free to use Category: Database/Warehouse 12

Tg

MISO 2012

Tg

MISO MISO About: MISO (Managing Information for Sequencing Operations) is a new open-source Lab Information Management System (LIMS) under development at TGAC, specifically designed for tracking next-generation sequencing experiments. Year of release: 2012 No altmetric.com data available. Download: http://www.tgac.ac.uk/miso/ Author: Robert Davey and Mario Caccamo Key publication: OS: Linux, Mac OS X and Windows Licence: GPL v3 Category: Database/Warehouse 10

Da

DALLIANCE BROWSER 2010

Da

DALLIANCE BROWSER DALLIANCE BROWSER About: Dalliance is a track-oriented genome viewer similar to Ensembl, UCSC, or GBrowse. However, it is a little different in operation because it uses recent extensions to web standards (HTML 5) to offer a higher level of interactivity than most previous genome viewers. Year of release: 2010 Download: http://www.biodalliance.org/ Author: Thomas Down DOI: 10.1093/bioinformatics/btr020 OS: Linux, Mac OS X and Windows Licence: BSD-Style licence. Category: Genome Browsers 07

Jb

JBROWSE 2007

Jb

JBROWSE JBROWSE About: JBrowse is a JavaScript genome browser with an emphasis on portability. Browse is the official successor to GBrowse. Year of release: 2007 Download: http://jbrowse.org/ Author: Rober Buels and Mitch Skinner DOI: 10.1101/gr.094607.109 OS: Linux and Mac OS X Licence: GNU Lesser GPL v 2.1 Category: Genome Browsers XX

Mb

MrBayes XX

Mb

MrBayes MrBayes About: MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. MrBayes uses Markov chain Monte Carlo (MCMC) methods to estimate the posterior distribution of model parameters. Year of release: XX No altmetric.com data available. Download: http://mrbayes.sourceforge.net/ Author: John Huelsenbeck, Bret Larget, Paul van der Mark, Fredrik Ronquist, Donald Simon and Maxim Teslenko. Key publication: http://mrbayes.sourceforge.net/commref_mb3.2.pdf OS: Macintosh, Windows, and UNIX Licence: Free software Category: ToolKits and APIs 04

Pn

PhastCons 2004

Pn

PhastCons PhastCons About: PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel). Year of release: 2004 No altmetric.com data available. Download: http://compgen.bscb.cornell.edu/phast/ Author: Adam Siepel, Melissa Hubisz and Katie Pollard Key publication: http://compgen.bscb.cornell.edu/~acs/phyhmm_with_apdx.pdf OS: Linux, Mac OS X and Windows Licence: BSD-style licence Category: ToolKits and APIs 08

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UGENE 2008

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UGENE UGENE About: Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. Year of release: 2008 Download: http://ugene.unipro.ru/ Author: Konstantin Okonechnikov; Olga Golosova; Mikhail Fursov DOI: 10.1093/bioinformatics/bts091 OS: Universal Licence: GPL v2 Category: ToolKits and APIs

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MUSCLE 2004

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MUSCLE MUSCLE About: MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Year of release: 2004 Download: http://www.drive5.com/muscle/ Author: Robert C. Edgar DOI: 10.1093/nar/gkh340 OS: Linux, MacOSX, Unix, Windows Licence: Freeware Category: Multiple Sequence Aligners 12

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PROT PAL 2012

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PROT PAL PROT PAL About: Prot Pal is a software tool for multiple sequence alignment, ancestral reconstruction, and measurement of indel rates on a phylogenetic tree. Year of release: 2012 No altmetric.com data available. Download: http://www.biowiki.org/ProtPal Author: Oscar Westesson and Ian Holmes Key publication: OS: Linux Licence: Free software Category: Multiple Sequence Aligners 05

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JIGSAW 2005

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JIGSAW JIGSAW About: JIGSAW is a program designed to use the output from gene finders, splice site prediction programs and sequence alignments to predict gene models. JIGSAW is available for all species. We have tested JIGSAW on Human, Rice (Oryza sativa), Arabidopsis thaliana, C. elegans, Brugia malayi, Cryptococcus neoformans, Entamoeba histolytica, Theileria parva, Aspergillus fumigatus, Plasmodium falciparum and Plasmodium yoelii. Year of release: 2005 Download: http://www.cbcb.umd.edu/software/jigsaw/ Author: Jonathan Edward Allen DOI: 10.1186/gb-2006-7-s1-s9 OS: Linux Licence: GNU gcc3.2 Category: Gene Prediction (mRNA) 08

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Tophat 2008

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Tophat Tophat About: 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. Year of release: 2008 Download: http://tophat.cbcb.umd.edu/ Author: Daehwan Kim, Geo Pertea, Cole Trapnell, Harold Pimentel, Ryan Kelley and Steven L Salzberg DOI: 10.1186/gb-2013-14-4-r36 OS: Linux, Mac Licence: Artistic Category: Sequence Tools 12

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RSEM 2012

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RSEM RSEM About: RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95% credibility interval estimates for expression levels. For visualization, It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Year of release: 2012 Download: http://deweylab.biostat.wisc.edu/rsem/ Author: Bo Li DOI: 10.1186/1471-2105-12-323 OS: Linux Licence: GPL Category: Sequence Tools 12

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Flexbar 2012

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Flexbar Flexbar About: Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided. Flexbar increases read mapping rates and improves genome and transcriptome assemblies. It supports next-generation sequencing data in fasta/q and csfasta/q format from Illumina, Roche 454, and the SOLiD platform. Year of release: 2012 Download: http://sourceforge.net/p/flexbar/wiki/Manual/ Author: Matthias Dodt, Johannes T. Roehr, Rina Ahmed, Christoph Dieterich DOI: 10.3390/biology1030895 OS: All Licence: GPL3 Category: Sequence Tools 12

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ENA 2012

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ENA ENA About: The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Year of release: 2012 No altmetric.com data available. Download: http://www.ebi.ac.uk/ena/home Author: Key publication: OS: Online Licence: Free Category: Database/Warehouse 11

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Pfam 2011

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Pfam Pfam About: The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Year of release: 2011 Download: http://pfam.sanger.ac.uk/ Author: L. Aravind, Adam Godik and Val Wood DOI: 10.1093/nar/gkr1065 OS: Linux Licence: Creative Commons Zero Category: Database/Warehouse 07

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SeqMonk 2007

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SeqMonk SeqMonk About: Year of release: 2007 No altmetric.com data available. Download: http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/ Author: Simon Andrews Key publication: OS: Linux, Mac OS X, Windows Licence: GPL v3 or later Category: Genome Browsers 10

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Savant 2010

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Savant Savant About: Savant is a next-generation genome browser designed for the latest generation of genome data. Year of release: 2010 Download: http://genomesavant.com/p/savant/index Author: Fiume M, Smith EJ, Brook A, Strbenac D, Turner B, Mezlini AM, Robinson MD, Wodak SJ, Brudno M. DOI: 10.1093/nar/gks427 OS: All Licence: Apache 2.0 Category: Genome Browsers XX

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Tripod XX

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Tripod Tripod About: Tripod is a user-friendly chemical genomics browser that is currently being developed by the informatics group at the NIH Chemical Genomics Center. The main goal of Tripod is to facilitate easy access to chemical and biological data in an intuitive, user-friendly tool. To this end, the development of Tripod is inspired by the ubiquitous iTunes software, whereby browsing and managing of media contents are being adapted to chemical and biological data. Year of release: XX No altmetric.com data available. Download: http://tripod.nih.gov/ Author: Ajit Jadhav et al. Key publication: OS: Online Licence: Category: Genome Browsers