Open Source Perl Bio-Informatics Software for Linux

SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools

MUMmer is a modular system for the rapid whole genome alignment of finished or draft sequence. This package provides an efficient suffix tree library, seed-and-extend alignment, SNP detection, repeat detection, and visualization tools.

HaploPainter - a pedigree and haplotypes drawing tool written in Perl/Tk. The software processes pedigree information in standard linkage formats combining haplotype information outputs from Simwalk, Genehunter, Allegro and Merlin.

Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.

A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/

PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.

The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format.

The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.

AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.

Integrated Hospital Information System. PHP,mySQL,PostgreSQL. Surgery, Nursing,Outpatient,Wards,Labs, Pharmacy, Security,Admission,Schedulers, Repair, Communication & more. Multilanguage, WYSIWYG forms, userconfig, embedded workbots. Modular & scalab

GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.

Life Science Identifier (LSID) resolution protocol, to locate biologically significant data over a network, within middle-ware providing a client A.P.I. for Life Science applications, and server software, for Industry data providers.

A bioinformatics tool to PRe-process and show INformation of SEQuence data. The tool is written in Perl and can be helpful if you want to filter, reformat, or trim your sequence data. It also generates basic statistics for your sequences.

The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.

MitoSAlt is a pipeline to identify large deletions and duplications in human and mouse mitochondrial genomes from next generation whole genome/exome sequencing data. The pipeline is capable of analyzing any circular genome in principle, as long as a proper configuration file is provided.

Source code from the Research Institute for Signals, Systems and Computational Intelligence http://fich.unl.edu.ar/sinc

FragGeneScan is an application for finding (fragmented) genes in short reads. It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013.

Maq is a set of programs that map and assemble fixed-length Solexa/SOLiD reads in a fast and accurate way.

The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads.

Traditional methods for isolation of microsatellites (SSRs) are often expensive and time consuming. Nowadays is easier and cheaper to obtain genomic data from next generation sequencing. Then, at least two software need to be applied in order to obtain SSR primers of SSR flanking sequences for PCR assays. Here we propose new software that allows the user to work with several sequences for PCR primer design in one step.

NOTE: The MView repository and web pages have moved to: https://github.com/desmid/mview https://desmid.github.io/mview/ Release tarballs will continue to be uploaded to SourceForge. ---- MView is a command line utility that extracts and reformats the results of a sequence database search or a multiple alignment, optionally adding HTML markup for web page layout. It can also be used as a filter to extract and convert searches or alignments to common formats. Inputs: - Sequence database search: BLAST, FASTA suites. - Multiple sequence alignment: CLUSTAL, HSSP, MSF, FASTA, PIR, MAF. Outputs: - HTML, FASTA, CLUSTAL, MSF, PIR, RDB (tab-separated). Found a bug? Please open an issue on the MView issue tracker at https://github.com/desmid/mview/issues or send an email to biomview@gmail.com.

MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Users could understand the underlying bins (genomes) of the microbes in their metagenomes by simply providing assembled metagenomic sequences and the reads coverage information or sequencing reads. For users' convenience MaxBin will report genome-related statistics, including estimated completeness, GC content and genome size in the binning summary page. Users could use MEGAN or similar software on MaxBin bins to find out the taxonomy of each bin after the binning process is finished. The most current version is 2.2.7. MaxBin was published on Microbiome journal (2:26)! Please cite the Microbiome paper if you use MaxBin in your work.

FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences.

Celera Assembler (CA) is a whole-genome shotgun (WGS) assembler for the reconstruction of genomic DNA sequence from WGS sequencing data.

EvidentialGene is a genome informatics project, "Evidence Directed Gene Construction for Eukaryotes", to construct high quality, accurate gene sets for animals and plants, developed by Don Gilbert at Indiana University, see http://arthropods.eugenes.org/EvidentialGene/ Construction refers to the combination of classical gene prediction, and more recent gene assembly (de-novo and genome-assisted) methods. The basic Evigene methods involve using available best-of-breed gene prediction and assembly software, combining all evidence for genes, from expressed sequences, genome assembly sequences, related species protein sequences, and any other, to annotate and score gene constructions. Over-produced constructions are classified by gene evidence for best qualities per "locus", including genome-aligned and gene-transcript aligned (genome-free) locus identification. All software developed for EvidentialGene is publicly available. See project wiki/blog for notes.