Molecular Science Software


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Molecular Science Software

  • PubNub: Realtime APIs, Global Infrastructure PubNub: Realtime APIs, Global Infrastructure Icon
    PubNub: Realtime APIs, Global Infrastructure Icon

    Harness the power of PubNub’s programmable APIs and robust global network to power realtime chat, geolocation, IoT, multiplayer games, and more.

    The realtime revolution is upon us. Users want data, and they want it now. Deliver the immersive, interactive experiences your audience craves with PubNub. Get to market quickly with pre-built SDKs, integrations, and serverless computing at the edge; then scale on a global network that delivers any message in under a quarter of a second with five 9’s reliability guaranteed.
  • Join us at Talend Connect! Join us at Talend Connect! Icon
    Join us at Talend Connect! Icon

    Get your tickets to the best data-driven event of the year!

    May 7 – May 9. Use discount code TCCommunity2018 for $200 off.

    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.



    Downloads: 20 This Week Last Update: See Project
  • Tahoe

    Tahoe is a research-oriented platform for the development of numerical methods and models for the simulation of complex material behavior.

    Downloads: 6 This Week Last Update: See Project
  • EASER Icon


    Ensembl Easy Sequence Retriever

    Maldonado E, Khan I, Philip S, Vasconcelos V, Antunes A (2013) EASER: Ensembl Easy Sequence Retriever. Evolutionary Bioinformatics, 9:487-490. doi: 10.4137/EBO.S11335.

    Downloads: 5 This Week Last Update: See Project
  • LMAP Icon


    Lightweight Multigene Analyses in PAML

    Maldonado E, Almeida D, Escalona T, Khan I, Vasconcelos V and Antunes A (2016) LMAP: Lightweight Multigene Analyses in PAML. BMC Bioinformatics, 17:354. doi: 10.1186/s12859-016-1204-5

    Downloads: 3 This Week Last Update: See Project
  • Get the Edge; Toad Edge Get the Edge; Toad Edge Icon
    Get the Edge; Toad Edge Icon

    Your next-gen toolset for MySQL database environments

    If you organization takes advantage of the cost-effective, flexible MySQL open source database platform, then you need a toolset that supports your commitment to open source relational databases. Toad Edge for MySQL has what you need and helps you ramp up on MySQL quickly, ensuring faster time to value.
  • Gaussian Output Tools

    Gaussian Output Tools is a package of simple scripts to extract data from Gaussian output files.

    Downloads: 2 This Week Last Update: See Project

    Elastic network models (ENMs) have been shown to generate the dominant functional equilibrium motions of biomolecules quickly and efficiently. MAVEN simplifies ENM generation, allows for diverse models to be used, and facilitates useful analyses.

    Downloads: 2 This Week Last Update: See Project
  • datasw Icon


    datasw, a tool for rapid processing of HPLC-SAXS data.

    Small-angle X-ray scattering (SAXS) in solution is a common low-resolution method which can efficiently complement high-resolution information obtained by crystallography or NMR. Sample monodispersity is key to reliable SAXS data interpretation and model building. Beamline setups with inline high-performance liquid chromatography (HPLC) are particularly useful for accurate profiling of heterogeneous samples. The program DATASW performs averaging of individual data frames from HPLC-SAXS experiment using a sliding window of a user-specified size, calculates overall parameters (I(0), Rg, Dmax and MW) and predicts the folding state (folded/unfolded) of the sample. Applications of DATASW are illustrated for several proteins with various oligomerization behaviors recorded at different beamlines. If you use DATASW in your work, please, cite: Shkumatov A.V. & Strelkov S.V. (2015) Acta Cryst. D71, 1347–1350

    Downloads: 2 This Week Last Update: See Project
  • mobcalPARSER Icon


    A cross-platform interface for the *.mfj file format.

    mobcalPARSER is a command line based PERL frontend/interface for MOBCAL with limited wrapper functionality. "MOBCAL - A Program to Calculate Mobilities" is available from Professor Martin F. Jarrold's webpage

  • 2D HF

    This is an extension to the standard 2D HF package (A Numerical Hartree-Fock Program for Diatomic Molecules by Jacek Kobus, Leif Laaksonen and Dage Sundholm) that adds some extra functionality.

    Downloads: 1 This Week Last Update: See Project
  • Use DigitalOcean to Build, Deploy & Scale Web Apps Use DigitalOcean to Build, Deploy & Scale Web Apps Icon
    Use DigitalOcean to Build, Deploy & Scale Web Apps Icon

    The ease and simplicity of DigitalOcean gives developers more time to build and innovate for their customers.

    Thousands of businesses and developers around the world use DigitalOcean to easily deploy, manage, and scale applications of any size with less infrastructure friction. Go from one to a thousand virtual servers in seconds. Also, we continue to add hundreds of in-depth tutorials to our documentation library and have an active online community to get the support you need to succeed.
  • Allelome.PRO

    A pipeline to define allele-specific genomic features

    Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analysed imprinted expression to give a complete picture of the “allelome” by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased biallelic or noninformative. Allelome.PRO offers increased sensitivity to analyse lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data.

    Downloads: 1 This Week Last Update: See Project
  • DIY Genomics

    DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

    Downloads: 1 This Week Last Update: See Project
  • Gvib

    GVIB is a user friendly package for vibrational analysis. Given a molecular geometry, it will calculate vibrational frequencies and intensities using anharmonic internuclear potential.

    Downloads: 1 This Week Last Update: See Project
  • Process_hits

    A fast efficient way of dealing with large amounts of Blast or Repeatmasker data.

    Downloads: 1 This Week Last Update: See Project
  • REDO

    REDO - RNA Editing Detection in Organelle

    REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple samples simultaneously and identify differential proportion of RNA editing events in different samples. Moreover, the genome variation can be easily removed by a subprogram in our package.

    Downloads: 1 This Week Last Update: See Project

    Reference based genome assembly and annotation for new genome

    This program can assemble and/or annotate genome for new genome and known genome upgrade using sequence alignment file (SAM or BAM format), sequence variant file (VCF format or five coloum table (tab-delimited, including chromosome, position, id, reference allele and alternative allele)) or new genome sequence file (FASTA format) based on reference genome sequence file (FASTA format) and annotation file (TBL, GTF, GFF, GFF3 or BED format).

    Downloads: 1 This Week Last Update: See Project
  • Assembly of mixed genomes

    Scripts used to assemble and deconvolute mixed mitochondrial genomes.

    Perl scripts used in the paper "Index-free de novo assembly and deconvolution of mixed mitochondrial genomes" by McComish BJ, Hills SFK, Biggs P and Penny D (2010) Genome Biology and Evolution 2:410-424.

    Downloads: 0 This Week Last Update: See Project
  • BIOperl Scripts for PHylogenetic Analyse

    Biospha is a suite of perl scripts based on bioperl toolkit intended to help researches to manage large sequence file. With BIOSPHA you can classify each sequence according to the NCBI taxonomy. You also can get all taxonomic info from a GI or Taxid.

    Downloads: 0 This Week Last Update: See Project
  • BODE: Bioinformatics ODds and Ends Icon

    BODE: Bioinformatics ODds and Ends

    A collection of bioinformatics-related software created by members of Cancer Research UK (possibly among others).

  • BibGlimpse MEDLINE Retriever

    Literature management tools typically require that bibliography is typed in by hand for each PDF reprint added. The BibGlimpse retriever presented here can automatically find Medline entries for arbitrary PDFs ( ).

    Downloads: 0 This Week Last Update: See Project
  • Cscape (Cancer Landscape)

    Cscape is an application for visualizing and navigating through data from a Reverse Phase Protein Microarray (RPMA). Cscape uses the Google Maps API to map the RPMA data on top of an image of a cancer cell and its associated pathways.

    Downloads: 0 This Week Last Update: See Project
  • Disco

    Disco (DIStribution of COnformations) is a software package for the estimation of solution conformations of organic molecules. It is rewritten form of NAMFIS method and can be used with the input files generated by Janocchio.

    Downloads: 0 This Week Last Update: See Project
  • EvalMSA

    Perl-based tool for evaluating multiple sequence alignments

    Downloads: 0 This Week Last Update: See Project
  • Downloads: 0 This Week Last Update: See Project
  • GPSR: A bioinformatics suite

    GPSR is a resource for genomics, proteomics and systems biology. The aim of this project is to build comprehensive resources in the field of bioinformatics.

    Downloads: 0 This Week Last Update: See Project
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