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            "name": "PyPop",
            "description": "Mature open-source software pipeline for population genomics.",
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                            "uri": "http://edamontology.org/operation_3196",
                            "term": "Genotyping"
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                            "uri": "http://edamontology.org/operation_3436",
                            "term": "Aggregation"
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                        {
                            "uri": "http://edamontology.org/operation_0488",
                            "term": "Linkage disequilibrium calculation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0252",
                            "term": "Peptide immunogenicity prediction"
                        }
                    ],
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                    "output": [],
                    "note": null,
                    "cmd": null
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            ],
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                "Command-line tool"
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                    "uri": "http://edamontology.org/topic_2830",
                    "term": "Immunoproteins and antigens"
                },
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                    "uri": "http://edamontology.org/topic_3796",
                    "term": "Population genomics"
                },
                {
                    "uri": "http://edamontology.org/topic_3056",
                    "term": "Population genetics"
                },
                {
                    "uri": "http://edamontology.org/topic_0102",
                    "term": "Mapping"
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                    "uri": "http://edamontology.org/topic_3930",
                    "term": "Immunogenetics"
                }
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                    "url": "https://github.com/alexlancaster/pypop",
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                {
                    "doi": "10.3389/fimmu.2024.1378512",
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                    "metadata": {
                        "title": "PyPop: a mature open-source software pipeline for population genomics",
                        "abstract": "Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop.",
                        "date": "2024-01-01T00:00:00Z",
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                        "authors": [
                            {
                                "name": "Lancaster A.K."
                            },
                            {
                                "name": "Single R.M."
                            },
                            {
                                "name": "Mack S.J."
                            },
                            {
                                "name": "Sochat V."
                            },
                            {
                                "name": "Mariani M.P."
                            },
                            {
                                "name": "Webster G.D."
                            }
                        ],
                        "journal": "Frontiers in Immunology"
                    }
                }
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                {
                    "name": "Alexander K. Lancaster",
                    "email": "alancaster@amberbiology.com",
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            "description": "Blazing fast toolkit to work with .hic and .cool files",
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                {
                    "uri": "http://edamontology.org/topic_0091",
                    "term": "Bioinformatics"
                },
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
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                            "uri": "http://edamontology.org/operation_3627",
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                            "data": {
                                "uri": "http://edamontology.org/data_0943",
                                "term": "Mass spectrum"
                            },
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                                    "uri": "http://edamontology.org/format_3244",
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                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0945",
                                "term": "Peptide identification"
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                            "format": [
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                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
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                "Windows"
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                    "note": null
                },
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                    "url": "https://github.com/524D/mzrecal/issues",
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                        "Issue tracker"
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                    "note": null
                }
            ],
            "download": [
                {
                    "url": "https://github.com/524D/mzrecal/releases",
                    "type": "Binaries",
                    "note": "Pre-build binaries for Linux (x86_64) and Windows",
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "https://github.com/524D/mzrecal/blob/master/README.md",
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            "publication": [
                {
                    "doi": "10.1093/bioinformatics/btab056",
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                    "version": "1.0.1",
                    "note": null,
                    "metadata": {
                        "title": "MzRecal: Universal MS1 recalibration in mzML using identified peptides in mzIdentML as internal calibrants",
                        "abstract": "In mass spectrometry-based proteomics, accurate peptide masses improve identifications, alignment and quantitation. Getting the most out of any instrument therefore requires proper calibration. Here, we present a new stand-alone software, mzRecal, for universal automatic recalibration of data from all common mass analyzers using standard open formats and based on physical principles.",
                        "date": "2021-09-01T00:00:00Z",
                        "citationCount": 1,
                        "authors": [
                            {
                                "name": "Marissen R."
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                            {
                                "name": "Palmblad M."
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            ],
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        {
            "name": "Jalview",
            "description": "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.",
            "homepage": "https://www.jalview.org/",
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                            "term": "Phylogenetic tree analysis"
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                            "uri": "http://edamontology.org/operation_3081",
                            "term": "Sequence alignment editing"
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                                "term": "Sequence alignment"
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                                    "term": "FASTA-aln"
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                                    "term": "GFF2-seq"
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                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
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                                    "uri": "http://edamontology.org/format_1948",
                                    "term": "nbrf/pir"
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                                    "term": "BioJSON (Jalview)"
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                                    "term": "BLC"
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                                "term": "Sequence alignment"
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                                    "uri": "http://edamontology.org/format_1948",
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                                    "uri": "http://edamontology.org/format_3464",
                                    "term": "JSON"
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                                    "uri": "http://edamontology.org/format_1961",
                                    "term": "Stockholm format"
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                                {
                                    "uri": "http://edamontology.org/format_1929",
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                    "cmd": null
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                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
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                {
                    "uri": "http://edamontology.org/topic_0092",
                    "term": "Data visualisation"
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                "Windows",
                "Mac"
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                    "url": "https://issues.jalview.org/",
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                    "type": [
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                    "note": "Latest development version"
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                    "url": "https://source.jalview.org/crucible/browse/jalview",
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                    "note": null
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                    "url": "https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw",
                    "type": [
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                    ],
                    "note": "YouTube training videos"
                }
            ],
            "download": [
                {
                    "url": "https://www.jalview.org/download",
                    "type": "Downloads page",
                    "note": null,
                    "version": null
                },
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                    "url": "https://www.jalview.org/download/source/",
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                    "note": null,
                    "version": null
                },
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                    "url": "https://www.jalview.org/download/?os=all",
                    "type": "Binaries",
                    "note": "Binaries for all platforms",
                    "version": null
                },
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                    "url": "https://www.jalview.org/favicon.svg",
                    "type": "Icon",
                    "note": null,
                    "version": null
                },
                {
                    "url": "https://www.jalview.org/download/other/jar/",
                    "type": "Binaries",
                    "note": "Executable JAR file",
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                    "metadata": {
                        "title": "OmicsSuite: a customized and pipelined suite for analysis and visualization of multi-omics big data",
                        "abstract": "With the advancements in high-throughput sequencing technologies such as Illumina, PacBio, and 10X Genomics platforms, and gas/liquid chromatography-mass spectrometry, large volumes of biological data in multiple formats can now be obtained through multi-omics analysis. Bioinformatics is constantly evolving and seeking breakthroughs to solve multi-omics problems; however, it is challenging for most experimental biologists to analyse data using command-line interfaces, coding, and scripting. Based on experience with multi-omics, we have developed OmicsSuite, a desktop suite that comprehensively integrates statistics and multi-omics analysis and visualization. The suite has 175 sub-applications in 12 categories, including Sequence, Statistics, Algorithm, Genomics, Transcriptomics, Enrichment, Proteomics, Metabolomics, Clinical, Microorganism, Single Cell, and Table Operation. We created the user interface with Sequence View, Table View, and intelligent components based on JavaFX and the popular Shiny framework. The multi-omics analysis functions were developed based on BioJava and 300+ packages provided by the R CRAN and Bioconductor communities, and it encompasses over 3000 adjustable parameter interfaces. OmicsSuite can directly read multi-omics raw data in FastA, FastQ, Mutation Annotation Format, mzML, Matrix, and HDF5 formats, and the programs emphasize data transfer directions and pipeline analysis functions. OmicsSuite can produce pre-publication images and tables, allowing users to focus on biological aspects. OmicsSuite offers multi-omics step-by-step workflows that can be easily applied to horticultural plant breeding and molecular mechanism studies in plants. It enables researchers to freely explore the molecular information contained in multi-omics big data (Source: https://github.com/OmicsSuite/, Website: https://omicssuite.github.io, v1.3.9).",
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                        "authors": [
                            {
                                "name": "Miao B.-B."
                            },
                            {
                                "name": "Dong W."
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                            {
                                "name": "Gu Y.-X."
                            },
                            {
                                "name": "Han Z.-F."
                            },
                            {
                                "name": "Luo X."
                            },
                            {
                                "name": "Ke C.-H."
                            },
                            {
                                "name": "You W.-W."
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                        ],
                        "journal": "Horticulture Research"
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                        "title": "Fast and sensitive taxonomic classification for metagenomics with Kaiju",
                        "abstract": "Metagenomics emerged as an important field of research not only in microbial ecology but also for human health and disease, and metagenomic studies are performed on increasingly larger scales. While recent taxonomic classification programs achieve high speed by comparing genomic k-mers, they often lack sensitivity for overcoming evolutionary divergence, so that large fractions of the metagenomic reads remain unclassified. Here we present the novel metagenome classifier Kaiju, which finds maximum (in-)exact matches on the protein-level using the Burrows-Wheeler transform. We show in a genome exclusion benchmark that Kaiju classifies reads with higher sensitivity and similar precision compared with current k-mer-based classifiers, especially in genera that are underrepresented in reference databases. We also demonstrate that Kaiju classifies up to 10 times more reads in real metagenomes. Kaiju can process millions of reads per minute and can run on a standard PC. Source code and web server are available at http://kaiju.binf.ku.dk.",
                        "date": "2016-04-13T00:00:00Z",
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                            {
                                "name": "Menzel P."
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                            {
                                "name": "Ng K.L."
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                            {
                                "name": "Krogh A."
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                        "title": "Comet: An open-source MS/MS sequence database search tool",
                        "abstract": "Proteomics research routinely involves identifying peptides and proteins via MS/MS sequence database search. Thus the database search engine is an integral tool in many proteomics research groups. Here, we introduce the Comet search engine to the existing landscape of commercial and open-source database search tools. Comet is open source, freely available, and based on one of the original sequence database search tools that has been widely used for many years. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.",
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                        "title": "A Deeper Look into Comet - Implementation and Features",
                        "abstract": "The Comet database search software was initially released as an open source project in late 2012. Prior to that, Comet existed as the University of Washington's academic version of the SEQUEST database search tool. Despite its availability and widespread use over the years, some details about its implementation have not been previously disseminated or are not well understood. We address a few of these details in depth and highlight new features available in the latest release. Comet is freely available for download at http://comet-ms.sourceforge.net or it can be accessed as a component of a number of larger software projects into which it has been incorporated. (Figure Presented).",
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