{"id":22314410,"url":"https://github.com/chrisarg/alien-seqalignment-last","last_synced_at":"2025-03-26T02:46:06.616Z","repository":{"id":229398785,"uuid":"766527647","full_name":"chrisarg/alien-seqalignment-last","owner":"chrisarg","description":"Sequence Alignment tool","archived":false,"fork":false,"pushed_at":"2024-03-24T03:32:34.000Z","size":38,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-25T11:50:21.042Z","etag":null,"topics":["bioinformatics","bioinformatics-analysis","bioinformatics-scripts","sequence","sequence-alignment"],"latest_commit_sha":null,"homepage":"","language":"Perl","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/chrisarg.png","metadata":{"files":{"readme":"README","changelog":"Changes","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2024-03-03T14:15:07.000Z","updated_at":"2024-03-24T04:32:47.000Z","dependencies_parsed_at":"2024-03-24T04:35:07.634Z","dependency_job_id":null,"html_url":"https://github.com/chrisarg/alien-seqalignment-last","commit_stats":null,"previous_names":["chrisarg/alien-seqalignment-last"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrisarg%2Falien-seqalignment-last","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrisarg%2Falien-seqalignment-last/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrisarg%2Falien-seqalignment-last/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrisarg%2Falien-seqalignment-last/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chrisarg","download_url":"https://codeload.github.com/chrisarg/alien-seqalignment-last/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245579582,"owners_count":20638676,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","bioinformatics-analysis","bioinformatics-scripts","sequence","sequence-alignment"],"created_at":"2024-12-03T22:09:58.199Z","updated_at":"2025-03-26T02:46:06.595Z","avatar_url":"https://github.com/chrisarg.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"NAME\n    Alien::SeqAlignment::edlib - find, build and install the last tools\n\nVERSION\n    version 0.02\n\nSYNOPSIS\n    To execute the last set of tools, you can use the following code:\n\n     use Alien::SeqAlignment::last;\n     use Env qw( @PATH );\n     unshift @PATH, Alien::SeqAlignment::last-\u003ebin_dir;\n\n    Now you can run the last tools as:\n\n     system Alien::SeqAlignment::last-\u003elastal (options);    \n     system Alien::SeqAlignment::last-\u003elastdb (options); \n     system Alien::SeqAlignment::last-\u003emaf_convert (options); \n     system Alien::SeqAlignment::last-\u003etrain (options); \n     system Alien::SeqAlignment::last-\u003esplit_or_splice (options); \n     system Alien::SeqAlignment::last-\u003esplit_or_splice_pe (options); \n     system Alien::SeqAlignment::last-\u003epe_probs (options);\n\nDESCRIPTION\n    This distribution provides last so that it can be used by other Perl\n    distributions that are on CPAN. The source code will be downloaded from\n    the last Gitlab repo, and if that fails it will use the location of a\n    fork by the author of this Perl module. The build provides the various\n    CLI tools in the last and last-pair-pe suites. Parallelization requires\n    the installation of the GNU parallel package. If this is not available,\n    the installation will terminate. In that case, install GNU Parallel from\n    https://www.gnu.org/software/parallel/ and re-attempt installation of\n    this Alien.\n\nMETHODS\n  lastal\n     Alien::SeqAlignment::last-\u003elastal\n\n    Returns the command name for running the CLI version of the last\n    aligner. The latter finds local alignments between query sequences, and\n    reference sequences that have been collected into a database using\n    lastdb.\n\n  dbbuild\n     Alien::SeqAlignment::last-\u003edbbuild\n\n    Returns the command name for the application that builds the database of\n    the reference sequences.\n\n  maf_convert\n     Alien::SeqAlignment::last-\u003emaf_convert\n\n    Interconverts the MAF format with other multiple alignment formats. The\n    formats currently supported are: axt, bed, blast, blasttab, chain, gff,\n    html, psl, sam, tab. Note that per the author of last, the blast format\n    is merely \"blast-like\", i.e. not identical to NCBI BLAST.\n\n  last_train\n     Alien::SeqAlignment::last-\u003elast_train\n\n    last-train finds the rates (probabilities) of insertion, deletion, and\n    substitutions between two sets of sequences. It thereby finds suitable\n    substitution and gap scores for aligning them.\n\n  split_or_splice\n     Alien::SeqAlignment::last-\u003esplit_or_splice\n\n    This commnd provides access to last-split, which finds \"split\n    alignments\" (typically for DNA) or \"spliced alignments\" (typically for\n    RNA).\n\n  split_or_splice_for_pe\n     Alien::SeqAlignment::last-\u003esplit_or_splice_for_pe\n\n    This commnd provides access to last-split, which finds \"split\n    alignments\" (typically for DNA) or \"spliced alignments\" (typically for\n    RNA). It specifically targets paired-end reads. last-split-pe is a\n    method that can split-align a short DNA read to a reference genome. It\n    achieves high accuracy by combining probabilistic alignments with\n    information from paired-end reads.\n\n  pe_probs\n     Alien::SeqAlignment::last-\u003epe_probs\n\n    This commnd provides access to last-pair-probs, which reads candidate\n    alignments of paired DNA reads to a genome, and:\n\n    * estimates the distribution of distances between paired reads, *\n    estimates the probability that each alignment represents the genomic\n    source of the read. These probabilities corresponds to a split alignment\n    of the pair end read.\n\nSEE ALSO\n    *   LAST \u003chttps://gitlab.com/mcfrith/last/-/tree/main\u003e\n\n        LAST: find \u0026 align related regions of sequences LAST is designed for\n        moderately large data (e.g. genomes, DNA reads, proteomes). It's\n        especially good at:\n\n        * Finding rearrangements and recombinations: the primary author\n        claims that last-split does that more rigorously than anything else.\n        * Finding DNA-versus-protein related regions, especially protein\n        fossils. * Unusual data, e.g. AT-rich DNA, because we can fit\n        parameters to the data and calculate significance. * Sensitive\n        DNA-DNA search, due to fitting, sensitive seeding, and calculating\n        significance.\n\n        It can also: indicate the confidence/uncertainty of each column in\n        an alignment, and use sequence quality data in a rigorous fashion.\n\n    *   last-split-pe\n        \u003chttps://bitbucket.org/splitpairedend/last-split-pe/wiki/Home\u003e\n\n        last-split-pe is a method that can split-align a short DNA read to a\n        reference genome. It achieves high accuracy by combining\n        probabilistic alignments with information from paired-end reads.\n\n    *   Alien\n\n        Documentation on the Alien concept itself.\n\n    *   Alien::Base \u003chttps://metacpan.org/pod/Alien::Base\u003e\n\n        The base class for this Alien. The methods in that class allow you\n        to use the static and the dynamic edlib library in your code.\n\n    *   Alien::Build::Manual::AlienUser\n        \u003chttps://metacpan.org/dist/Alien-Build/view/lib/Alien/Build/Manual/A\n        lienUser.pod\u003e\n\n        Detailed manual for users of Alien classes.\n\n    *   Bio::SeqAlignment \u003chttps://metacpan.org/pod/Bio::SeqAlignment\u003e\n\n        A collection of tools and libraries for aligning biological\n        sequences from within Perl.\n\nAUTHOR\n    Christos Argyropoulos \u003cchrisarg@gmail.com\u003e\n\nCOPYRIGHT AND LICENSE\n    This software is copyright (c) 2024 by Christos Argyropoulos.\n\n    This is free software; you can redistribute it and/or modify it under\n    the same terms as the Perl 5 programming language system itself.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchrisarg%2Falien-seqalignment-last","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchrisarg%2Falien-seqalignment-last","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchrisarg%2Falien-seqalignment-last/lists"}