Lambda

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Lambda: the Local Aligner for Massive Biological DatA

Lambda is a local aligner optimized for many query sequences and searches in protein space. It is compatible to BLAST, but much faster than BLAST and many other comparable tools.

Downloads are available from the sidebar on the left. Lambda is Free and open source software, so you can use it for any purpose, free of charge. However certain conditions apply when you (re-)distribute or modify Lambda, please respect the license. Also, please cite the publication if you use Lambda anywhere in your academic work. Thank you!

The manual, build instructions and much more are available in the: ━━━┥ WIKI ┝━━━

Publication

Lambda: the local aligner for massive biological data; Hannes Hauswedell, Jochen Singer, Knut Reinert; Bioinformatics 2014 30 (17): i349-i355; doi: 10.1093/bioinformatics/btu439

News

2017-06-29: Release of 1.9.3

Version 1.9.3 has just been released. It is a pre-release of the development branch and offers numerous bug-fixes, additions for taxonomic analysis, speed improvements for short sequences and a reduction of the required memory. Beyond that there are multiple usability improvements including stricter argument parsing, better exception handling and a check of the available memory against the estimated amount required so that users are warned early on if they might run out during a long run. Lambda now informs you when new versions become available so that you don't miss future updates. The index format has changed and is not compatible to previous versions.

2017-01-10: Release of 1.9.2

Version 1.9.2 has just been released. It is a pre-release of the development branch and offers new features for taxonomic analysis, including taxonomic ID retrieval and annotation, as well as taxonomic binning via computation of the lowest common ancestor (LCA) of all matches of each query sequence. More information on these features is available in the Wiki. The release also includes a lot of changes to core algorithms to improve performance, however, these are not yet active by default. Please provide feedback on the new release, especially the new features! But also bear in mind that the 1.9.* series might be less stable than 1.0.* and that you need to re-create the index files.

2017-01-09: Release of 1.0.1

Version 1.0.1 has just been released. It contains minor fixes and performance improvements. It is fully compatible to the 0.9.* and 1.0.* series.

2016-08-18: Release of 1.9.0

Version 1.9.0 has just been released. It is a pre-release of the development branch and comes with very significant performance improvements. We are not publishing any numbers, yet, because it is still in development, but you should see very big differences immediately. Of course we are interested in your feedback so please try out the new release! But also bear in mind that it might be less stable than 1.0.0 and that you need to re-create the index files.

2016-08-18: Release of 1.0.0

Version 1.0.0 has just been released. It contains minor fixes and performance improvements. It is fully compatible to the 0.9.* series.

2016-08-18: Git-History invalidated

There were some significant changes to the git repository, SeqAn is now only included as a git submodule. This means that previous clones of the git repository are no longer valid and must be force-updated or cleanly re-cloned. Clone with the --recursive parameter if you don't have SeqAn installed system-wide.

2016-04-08: Release of 0.9.4

Version 0.9.4 has just been released. It contains minor SAM/BAM fixes and additions, and it now runs on OpenBSD. Lambda can now also be built with Clang (as of version 3.8) and the Intel Compiler (as of version 16.0.2). If there are no serious bugs, this version will soon become 1.0 and development of the new feature branch will begin.

2015-12-11: Release of 0.9.3

Version 0.9.3 has just been released. This is mostly a bug-fix release. We have also added app tests and continuous integration builds to improve the quality of Lambda and spot issues more quickly. Happy holiday season to all users who are affected :-)

2015-11-27: Release of 0.9.2

Version 0.9.2 has just been released. We have implemented (long-awaited) support for the SAM and BAM formats! And documentation on the different formats and their options has been added to the wiki. The indexer now truncates sequence IDs by default which results in smaller indexes. If you use the pairwise format (.m0) you might want to change this since your output files will only contain the shortened IDs otherwise; all other formats are not effected (they truncate the IDs anyway). Head over to the releases for a full list of changes and the downloads. Updated index files will be created next week (but old indexes are compatible).

2015-10-23: Release of 0.9.1

Version 0.9.1 has just been released. There is now support for memory-mapped file access to the database which enables sharing the memory between multiple instances of LAMBDA running on the same server. Also the construction of the index now uses a different algorithm which is faster and more memory efficient. See the Changelog for details. Users who built 0.9.0 from Source, please be aware that optimizations where not turned on by default, so please update to 0.9.1 and rebuild. Users of our binaries are not affected.

2015-09-15: Indexes prebuilt for 0.9.*

There are now pre-built indexes for NR, the Uniref databases and the Uniprot databases available in the wiki.

2015-09-14: Release of 0.9.0

I am pleased to announce the availability of lambda-0.9.0. This is the first release based off SeqAn 2.0 with many bug-fixes and new features. See the Changelog for details. Please note that the indexes created with older versions are not compatible.