{"id":18243924,"url":"https://github.com/gaurav/taxondna","last_synced_at":"2025-07-27T07:40:37.198Z","repository":{"id":542580,"uuid":"172527","full_name":"gaurav/taxondna","owner":"gaurav","description":"Taxonomy-aware DNA sequence processing toolkit","archived":false,"fork":false,"pushed_at":"2025-03-14T18:56:29.000Z","size":102688,"stargazers_count":31,"open_issues_count":73,"forks_count":10,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-03-29T12:12:31.122Z","etag":null,"topics":["java","maven","sequencematrix","speciesidentifier"],"latest_commit_sha":null,"homepage":"http://www.ggvaidya.com/taxondna/","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/gaurav.png","metadata":{"files":{"readme":"README.txt","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2009-04-10T05:17:31.000Z","updated_at":"2025-03-14T18:56:34.000Z","dependencies_parsed_at":"2022-07-04T13:31:08.161Z","dependency_job_id":null,"html_url":"https://github.com/gaurav/taxondna","commit_stats":null,"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gaurav%2Ftaxondna","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gaurav%2Ftaxondna/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gaurav%2Ftaxondna/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/gaurav%2Ftaxondna/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/gaurav","download_url":"https://codeload.github.com/gaurav/taxondna/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247184948,"owners_count":20897860,"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":["java","maven","sequencematrix","speciesidentifier"],"created_at":"2024-11-05T09:04:17.887Z","updated_at":"2025-04-04T13:30:57.773Z","avatar_url":"https://github.com/gaurav.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"Readme for TaxonDNA 1.8\r\n=======================\r\n\r\nCONTENTS\r\n1. \tSystem requirements\r\n2.      Individual tools\r\n3.      Building software\r\n4. \tMemory requirements\r\n5. \tFile formats\r\n6. \tFurther information\r\n7.      References\r\n\r\n1. SYSTEM REQUIREMENTS\r\n\r\nTaxonDNA is written entirely in Java, with its interface written using \r\neither Java AWT or Swing. Its only requirement is a standard Java VM - \r\nexcept that since TaxonDNA 1.6 we've given up supporting Java 1.4, so \r\nyou'll need to have atleast Java 1.5 since then.\r\n\r\nThere are a long list of bugs [1], some of which prevent TaxonDNA from\r\nworking well on multiple platforms. Note particularly UI-related issues:\r\nsome UI elements only work on particular platforms, although we try to\r\nwork around them as well as we can.\r\n\r\n2. INDIVIDUAL TOOLS\r\n\r\nTaxonDNA consists of three tools - Species Identifier [2], SequenceMatrix,\r\nand GenBank Explorer (still in beta). JNLP files for the first two\r\nare available in this repository (but you'll have to get someone to\r\nthe latest JAR files to Sourceforge), as well as MS-DOS Batch files,\r\nif you prefer those. You should be able to get GBX working by running:\r\n        cd build/classes\r\n        java -Xmx1024M com.ggvaidya.TaxonDNA.GenBankExplorer.GenBankExplorer\r\n\r\n3. BUILDING SOFTWARE\r\n\r\nYou will need the javac compiler, a copy of the Java runtime and the\r\nAnt build tool in order to build TaxonDNA. The Ant build.xml should\r\ncontain all the necessary instructions to build any of the components\r\nyou need. A plain \"ant\" will compile all the source; additional\r\ntargets are available to package TaxonDNA.\r\n\r\n4. MEMORY REQUIREMENTS\r\n\r\nTaxonDNA uses an unfortunately a large amount of memory per sequence. \r\nIt can handle larger files fairly well, but by default, Java\r\napplications are limited to 64mb. You will need to use the '-Xmx' \r\noption to increase your memory usage. The easiest way to do this is, \r\nat the command line, to enter:\r\n\tjava -Xmx1024M -jar TaxonDNA.jar\r\n\r\nYou might also have to adjust the value of 1024 megabytes depending \r\non the size of your dataset and on the memory available to your \r\ncomputer. Java will refuse to run if the Xmx value specified is too\r\nlarge. Also, if TaxonDNA.jar is not in the directory specified, you \r\nmight need to enter the complete path to TaxonDNA, as so:\r\n\tjava -Xmx1024M -jar C:\\TaxonDNA\\TaxonDNA.jar\r\n\r\nIf the program runs out of memory while running, it will appear to \r\n\"hang\" and become completely unresponsive. There is at present no \r\nway to recover from this state. You'll want to increase your memory\r\nsetting using \"-Xmx\" as shown above.\r\n\r\nPlease note that trying to load a sequences file larger than the \r\nmemory size specified (i.e. 1024 mb in the above example) will also \r\nresult in the program hanging. We have tested this program with a \r\nfile of 2,185 sequences with 2,664 base pairs, and it has been known \r\nto work on datasets upto 8,000 sequences long. Please let us know if \r\nmemory size is an issue for you, and we will try to incorporate \r\nworkarounds in future versions.\r\n\r\n5. FILE FORMATS\r\n\r\nThis program can handle input in FASTA, MEGA, Nexus and TNT formats.\r\nGenBank support is provided through the GenBankExplorer. FASTA\r\nis our oldest supported format, and most of the tools are designed \r\nto accept sequences from NCBI GanBank (exported as FASTA) as input. \r\nIt attempts to guess the species name from the FASTA title string,\r\nand considers hyphens ('-') as gaps, and question marks ('?') as \r\nmissing data (incidently, if you use a very different gap/missing \r\nsyntax, you could use Nexus as an intermediate format, since it \r\nsupports defining your own gap/missing data specifier.\r\n\r\n6. FURTHER INFORMATION\r\n\r\nIf you need more information about this program, or have any other \r\nquestions, queries or bug reports to make, please contact us, either \r\nvia *any* of our websites:\r\n\thttp://taxondna.sf.net/\r\n        http://code.google.com/p/taxondna/\r\n        http://github.com/gaurav/taxondna/\r\n        http://groups.google.com/group/taxondna\r\n\r\nor by e-mail at\r\n\tgaurav AT ggvaidya DOT com.\r\n\r\n7. REFERENCES\r\n[1] TaxonDNA bug list at http://code.google.com/p/taxondna/issues/list\r\n[2] Meier, R., Kwong, S., Vaidya, G., Ng, Peter K. L. (2006) \r\n    DNA Barcoding and Taxonomy in Diptera: a Tale of High Intraspecific \r\n    Variability and Low Identification Success. \r\n    Systematic Biology, 55: 715-728.\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgaurav%2Ftaxondna","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgaurav%2Ftaxondna","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgaurav%2Ftaxondna/lists"}