{"id":29224590,"url":"https://github.com/sing-group/alter","last_synced_at":"2025-07-03T06:07:25.495Z","repository":{"id":88302475,"uuid":"72340303","full_name":"sing-group/ALTER","owner":"sing-group","description":"ALignment Transformation EnviRonment","archived":false,"fork":false,"pushed_at":"2018-05-08T17:12:18.000Z","size":1005,"stargazers_count":7,"open_issues_count":0,"forks_count":1,"subscribers_count":5,"default_branch":"master","last_synced_at":"2023-10-25T22:29:41.243Z","etag":null,"topics":["alignment-files","format-conversion-tool","format-converter","java","java-bioinformatics","phylogenetics"],"latest_commit_sha":null,"homepage":"http://www.sing-group.org/ALTER/","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sing-group.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING.LESSER","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-10-30T09:30:42.000Z","updated_at":"2023-08-15T02:27:20.000Z","dependencies_parsed_at":null,"dependency_job_id":"26761d29-fa3a-49f8-9631-03a3f288571f","html_url":"https://github.com/sing-group/ALTER","commit_stats":null,"previous_names":[],"tags_count":1,"template":null,"template_full_name":null,"purl":"pkg:github/sing-group/ALTER","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2FALTER","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2FALTER/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2FALTER/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2FALTER/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sing-group","download_url":"https://codeload.github.com/sing-group/ALTER/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2FALTER/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263271501,"owners_count":23440396,"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":["alignment-files","format-conversion-tool","format-converter","java","java-bioinformatics","phylogenetics"],"created_at":"2025-07-03T06:07:24.083Z","updated_at":"2025-07-03T06:07:25.470Z","avatar_url":"https://github.com/sing-group.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"ALTER Project\n=============\n\n# What is ALTER\nALTER stands for (ALignment Transformation EnviRonment) and it is a set of software components to transform between [Multiple Sequence Alignment](http://en.wikipedia.org/wiki/Multiple_sequence_alignment) file formats.\n\nALTER difers from other similar tools in the way that is \"program-oriented\" instead of simply \"format-oriented\", that is, when you convert between one format into another, you have to specify which program did generate your input file and which program will consume your generated file. This is because many programs does not follow the exact format standard, making custom asumptions about it, so tranforming directly between standard formats does not always ensure that your produced file will be processed by the next program correctly.\n\n# ALTER software components\nALTER contains a set of components:\n\n1. A core library.\n2. A command line interface.\n3. A desktop graphical user interface (GUI).\n4. A web interface (a running instance is here: [http://sing.ei.uvigo.es/alter](http://sing.ei.uvigo.es/alter)).\n\n# Building ALTER and running from source\n\n## Build\nBefore starting, you have to download and install:\n\n1. Git tool for cloning the last version\n2. A Java Compiler and tool\n3. The Maven tool\n\nAnd now, you can download and build it by performing:\n\n```\ngit clone https://github.com/sing-group/ALTER.git\ncd ALTER\nmvn package\n```\n\n## Running the desktop graphical user interface\n```\njava -jar alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar\n```\n\n## Running the command line user interface\n```\njava -jar alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar help\n```\n\n## Running the web user interface in your own machine\n1. Download a jetty-runner.jar, which is a server of Java Web applications. For example, download the 9.4.0RC1 version from here [here](http://central.maven.org/maven2/org/eclipse/jetty/jetty-runner/9.4.0.RC1/jetty-runner-9.4.0.RC1.jar)\n2. Place the jetty-runner-9.4.0.RC1.jar inside your ALTER folder, and the run:\n```\njava -jar jetty-runner-9.4.0.RC1.jar alter-web/target/alter-web-1.3.4.war\n```\n\nOnce the server has started, surf to [http://localhost:8080](http://localhost:8080/)\n\n# Use the core library in your projects\n\n## Include the library in your project\n\n### Maven project (recommended)\nImport our repository into your pom.xml file\n```\n\u003cproject\u003e\n    [...]\n    \u003crepositories\u003e\n        [...]\n         \u003crepository\u003e\n            \u003cid\u003esing-repository\u003c/id\u003e\n            \u003cname\u003eSING repository\u003c/name\u003e\n            \u003curl\u003ehttp://sing.ei.uvigo.es/maven2\u003c/url\u003e\n        \u003c/repository\u003e\n        [...]\n    \u003c/repositories\u003e\n    [...]\n    \u003cdependencies\u003e\n        [...]\n    \t\u003cdependency\u003e\n            \u003cgroupId\u003ees.uvigo.ei.sing\u003c/groupId\u003e\n            \u003cartifactId\u003ealter-lib\u003c/artifactId\u003e\n            \u003cversion\u003e1.3.4\u003c/version\u003e\n        \u003c/dependency\u003e\n    \t[...]\n    \u003c/dependencies\u003e\n\u003c/project\u003e\n```\n\n\n\n### Include the .jar inside your classpath\nYou have to include the alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar file in your classpath\n\n## Make a sequence conversion inside your Java code\nHere it is an example to convert a NEXUS file to ALN.\n\n```java\npackage testalter;\n\nimport es.uvigo.ei.sing.alter.converter.Converter;\nimport es.uvigo.ei.sing.alter.converter.DefaultFactory;\nimport es.uvigo.ei.sing.alter.parser.ParseException;\n\nimport java.io.IOException;\nimport java.nio.file.Files;\nimport java.nio.file.Paths;\n\npublic class TestAlter {\n\n\tpublic static void main(String[] args) throws IOException {\n\t\tConverter converter = new DefaultFactory().getConverter(\n            \"Linux\", \t// Input operating system (Linux, MacOS or Windows)\n\t\t\t\"clustal\", \t// Input program (Clustal, MAFFT, MUSCLE, PROBCONS or TCoffee)\n\t\t\t\"NEXUS\",\t// Input format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)\n\t\t\tfalse,\t\t// Autodetect format (other input options are omitted)\n\t\t\tfalse,\t\t// Collapse sequences to haplotypes\n\t\t\ttrue,\t\t// Treat gaps as missing data when collapsing\n\t\t\tfalse,\t\t// Count missing data as differences when collapsing\n\t\t\t0,\t\t\t// Connection limit (sequences differing at \u003c= l sites will be collapsed) (default is l=0)\n\t\t\t\"windows\",\t// Output operating system (Linux, MacOS or Windows)\n\t\t\t\"general\",\t// Output program (jModelTest, MrBayes, PAML, PAUP, PhyML,\n\t\t\t\t\t\t// ProtTest, RAxML, TCS, CodABC,\n\t\t\t\t\t\t// BioEdit, MEGA, dnaSP, Se-Al, Mesquite, SplitsTree, Clustal, MAFFT,\n\t\t\t\t\t\t// MUSCLE, PROBCONS, TCoffee, Gblocks, SeaView, trimAl or GENERAL)\n\t\t\t\"aln\",  \t// Output format (ALN, FASTA, GDE, MEGA, MSF, NEXUS, PHYLIP or PIR)\n\t\t\tfalse,\t\t// Low case output\n\t\t\tfalse,\t\t// Output residue numbers (only ALN format)\n\t\t\tfalse,\t\t// Sequential output (only NEXUS and PHYLIP formats)\n\t\t\tfalse,\t\t// Output match characters\n\t\t\t\"MyConverterApp\" // identifier for log messages\n\t\t);\n\n\n\t\ttry {\n\t\t\tString inputSequence = new String(Files.readAllBytes(Paths.get(\"input.nexus\")));\n\n\t\t\tString converted = converter.convert(inputSequence);\n\n\t\t\tSystem.out.println(\"converted file:\");\n\t\t\tSystem.out.println(converted);\n\n\t\t} catch (ParseException e) {\n\t\t\tSystem.err.println(\"the input file seems to contain errors\");\n\t\t\te.printStackTrace();\n\t\t}\n\n\t}\n}\n```\n\n# Development Team\nThe ALTER development team is:\n\n* Daniel Glez-Peña.\n* Daniel Gómez-Blanco.\n* Miguel Reboiro-Jato.\n* Florentino Fdez-Riverola.\n* David Posada.\n\n# Citing ALTER\nIf you are using ALTER in your research work, please cite us:\n\nD. Glez-Peña; D. Gómez-Blanco; M. Reboiro-Jato; F. Fdez-Riverola; D. Posada (2010) ALTER: program-oriented format conversion of DNA and protein alignments. Nucleic Acids Research. Web Server issue. ISSN: 0305-1048\n[http://dx.doi.org/10.1093/nar/gkq321](http://dx.doi.org/10.1093/nar/gkq321)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Falter","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsing-group%2Falter","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Falter/lists"}