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anydbm-branch bio_index_ace hmmer-bug3264 issues/124 master merge_root_into_live reorganization_2.x storable_db topic/adsj-seqobj-return topic/assembly-less topic/bug-2701 topic/bug3039 topic/cached_locations topic/cjfields_psl_fixes topic/cjfields_standard_lib topic/dbolser-biocoord_pair_tests_redo topic/gsoc_2010 topic/leto_interpro_cite topic/leto_interpro_get_dbxref topic/local_build topic/most_testiest topic/phyloxml_output_refac topic/rework-db-taxonomy topic/sf_lite_fixes topic/switch_sf_annotated topic/taxdb-to-sqlite2 topic/tree_api_refresh topic/tree_dbsqlite_memoryfix topic/yinjun111-simplealign v1.6.x
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This is the README file for the Bioperl central distribution, Version 1.0.0 # $Id$ o Getting Started Thanks for downloading this distribution! For tutorials see Bioperl's bptutorial.pl or the online Bioperl tutorial at http://www.pasteur.fr/recherche/unites/sis/formation/bioperl. For information on databases and Bioperl see biodatabases.pod. To look at example code browse the examples/ and scripts/ directories, and look at bioperl.pod for a descriptions of all these scripts. The bioperl.pod file also gives a overview of the history and purpose of Bioperl. For a discussion of issues in design and development please see biodesign.pod, recommended for those who want to contribute code. And for a list of OS's and versions that are known to support Bioperl see the PLATFORMS file. For info on Bioperl read on! o About Bioperl Bioperl is an association of developers of public domain Perl tools for computational molecular biology. Our website http://bioperl.org provides an online resource for modules, scripts, and web links for developers of Perl-based software for life science research. o Survey We'd like to hear your feedback. If you are using this toolkit for the first time or you are bioperl guru or somewhere in between, please consider filling out the survey to help us generate user statistics. We will post the tabulated results on the website as soon as we are able to process them and recieve enough responses. All individual responses including comments and optional email name and organization will be keep confidential for use only by the Open Bioinformatics Foundation. You responses will greatly assist the bioperl project and its ability to expand towards new problems in bioinformatics and computational biology. You can access the survey at http://www.bioperl.org/survey.html or follow the links to the Bioperl Survey from the bioperl website at http://bioperl.org. o Contact info Bioperl developers: firstname.lastname@example.org There's quite a variety of tools available in Bioperl, and more are added all the time. If the tool you're looking for isn't described in the documentation please write us, it could be undocumented or in process. Project website : http://bioperl.org Project FTP server: bioperl.org (anonymous FTP ok) Bug reports : http://bioperl.org/bioperl-bugs/ email@example.com Please send us bugs, in particular about documentation which you think is unclear or problems in installation. We are also very interested in functions which don't work the way you think they do! Please see the AUTHORS file for the complete list of bioperl developers and contributors. Please see the INSTALL document for installation instructions. o About the directory structure The bioperl directory structure is organised as follows: Bio/ - Bioperl modules models/ - DIA drawing program generated OO UML for bioperl classes t/ - Perl built-in tests t/data/ - Data files used for the tests - provides good data examples for those new to bioinformatics data. scripts/ - Resuable scripts that use bioperl, some organisation in attempted here (i.e. das contains das related scripts) scripts/contributed - User submissions of useful scripts not necessarily integrated into bioperl. Please see the README in this directory. examples/ - Example code snippets o Documentation The "meta" documentation can be found in the bioperl.pod file. This should be the starting point for you to read about what bioperl is, how to use it and who wrote it. The bptutorial.pl file is a POD formatted tutorial document that contains useful information for new and existing Bioperl users. This file also contains a number of useful scripts that the student of Bioperl may want to examine. Use your favorite pod2* translator turn it into the format of choice or view it directly via perldoc. For example, go perldoc bioperl or in this directory go pod2text bioperl.pod | more pod2text bptutorial.pl | more pod2html, which comes with Perl, can be used to create web-browser navigable documentation files. Individual *.pm modules have their own embedded POD documentation as well. A complete set of hyperlinked POD, or module, documentation is available at http://www.bioperl.org. The most up-to-date Remember 'perldoc' is your friend. You can use this to read any file containing POD formatted documentation without needing any type of translator. There is also an online course written at the Pasteur Institute. See: http://www.pasteur.fr/recherche/unites/sis/formation/bioperl. Useful documentation, in the form of example code, can also be found in the scripts/ and examples/ directories. The current collection includes scripts that run BLAST and retrieve full "Subject" sequences, make primers, retrieve ESTs based on tissue, align protein to nucleotide sequence, run GENSCAN on multiple sequences, and much more! See bioperl.pod for a complete listing. o Releases Bioperl releases are always available from the website http://www.bioperl.org or by FTP from ftp://bioperl.org. Each release is tested with the test suite and cross-tested on a number of different platforms. See the PLATFORMS file for more information on a specific platform. All efforts are made to release a bug-free package, however any known bugs in a release will be documented in the BUGS file. See the Changes file for a listing of what features have been added or what APIs have changed between releases. All odd numbered point releases will be developer releases and even point releases are stable releases.