Loading .gitignore +3 −3 Original line number Diff line number Diff line Loading @@ -52,6 +52,6 @@ build/ .idea Makefile diamond src/extra/benchmark.cpp src/extra/test.cpp src/extra/seed_stat.cpp No newline at end of file src/extra/ .vs/ CMakeSettings.json .travis.yml 0 → 100644 +8 −0 Original line number Diff line number Diff line matrix: include: - language: c++ compiler: g++ script: mkdir build; cd build; cmake ..; make - language: c++ compiler: clang script: mkdir build; cd build; cmake ..; make CMakeLists.txt +11 −1 Original line number Diff line number Diff line Loading @@ -10,6 +10,8 @@ if(BUILD_STATIC) set(CMAKE_EXE_LINKER_FLAGS "-static") endif() set(CMAKE_CXX_STANDARD 11) if(CMAKE_BUILD_MARCH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${CMAKE_BUILD_MARCH}") else() Loading @@ -24,7 +26,11 @@ find_package(ZLIB REQUIRED) find_package(Threads REQUIRED) set(CMAKE_BUILD_TYPE Release) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized -Wno-deprecated-declarations -Wno-ignored-attributes -Wno-unused-variable") if(WIN32) add_definitions(-D_CRT_SECURE_NO_WARNINGS) else() set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable") endif() include_directories( "${CMAKE_SOURCE_DIR}/src" Loading Loading @@ -113,6 +119,10 @@ add_executable(diamond src/run/main.cpp src/util/memory/memory_pool.cpp src/data/seed_array.cpp src/output/paf_format.cpp src/util/system/system.cpp src/run/cluster.cpp src/util/algo/greedy_vortex_cover.cpp src/util/algo/greedy_vortex_cover_weighted.cpp ) if(EXTRA) Loading LICENSE +112 −57 Original line number Diff line number Diff line GNU AFFERO GENERAL PUBLIC LICENSE Version 3, 19 November 2007 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU Affero General Public License is a free, copyleft license for software and other kinds of works, specifically designed to ensure cooperation with the community in the case of network server software. The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, our General Public Licenses are intended to guarantee your freedom to the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you Loading @@ -24,34 +26,44 @@ them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things. Developers that use our General Public Licenses protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License which gives you legal permission to copy, distribute and/or modify the software. A secondary benefit of defending all users' freedom is that improvements made in alternate versions of the program, if they receive widespread use, become available for other developers to incorporate. Many developers of free software are heartened and encouraged by the resulting cooperation. However, in the case of software used on network servers, this result may fail to come about. The GNU General Public License permits making a modified version and letting the public access it on a server without ever releasing its source code to the public. The GNU Affero General Public License is designed specifically to ensure that, in such cases, the modified source code becomes available to the community. It requires the operator of a network server to provide the source code of the modified version running there to the users of that server. Therefore, public use of a modified version, on a publicly accessible server, gives the public access to the source code of the modified version. An older license, called the Affero General Public License and published by Affero, was designed to accomplish similar goals. This is a different license, not a version of the Affero GPL, but Affero has released a new version of the Affero GPL which permits relicensing under this license. To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others. For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it. For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software. For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions. Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users. Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free. The precise terms and conditions for copying, distribution and modification follow. Loading @@ -60,7 +72,7 @@ modification follow. 0. Definitions. "This License" refers to version 3 of the GNU Affero General Public License. "This License" refers to version 3 of the GNU General Public License. "Copyright" also means copyright-like laws that apply to other kinds of works, such as semiconductor masks. Loading Loading @@ -537,45 +549,35 @@ to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Remote Network Interaction; Use with the GNU General Public License. Notwithstanding any other provision of this License, if you modify the Program, your modified version must prominently offer all users interacting with it remotely through a computer network (if your version supports such interaction) an opportunity to receive the Corresponding Source of your version by providing access to the Corresponding Source from a network server at no charge, through some standard or customary means of facilitating copying of software. This Corresponding Source shall include the Corresponding Source for any work covered by version 3 of the GNU General Public License that is incorporated pursuant to the following paragraph. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU General Public License into a single under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the work with which it is combined will remain governed by version 3 of the GNU General Public License. but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU Affero General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU Affero General Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU Affero General Public License, you may choose any version ever published GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU Affero General Public License can be used, that proxy's versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Loading Loading @@ -617,3 +619,56 @@ Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. <one line to give the program's name and a brief idea of what it does.> Copyright (C) <year> <name of author> This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>. Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: <program> Copyright (C) <year> <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <https://www.gnu.org/licenses/>. The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <https://www.gnu.org/licenses/why-not-lgpl.html>. README.md 0 → 100644 +92 −0 Original line number Diff line number Diff line Introduction ============ DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are: - Pairwise alignment of proteins and translated DNA at 500x-20,000x speed of BLAST. - Frameshift alignments for long read analysis. - Low resource requirements and suitable for running on standard desktops or laptops. - Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification. Keep posted about new developments by following me on [Twitter](https://twitter.com/bbuchfink). [](https://travis-ci.org/bbuchfink/diamond) [](https://anaconda.org/bioconda/diamond)  [](https://anaconda.org/bioconda/diamond) Quick start guide ================= Please read the [manual](https://github.com/bbuchfink/diamond/raw/master/diamond_manual.pdf) for detailed installation and usage instructions. This demonstrates a quick example for setting up and using the program on Linux. Installing the software on your system may be done by downloading it in binary format for immediate use: wget http://github.com/bbuchfink/diamond/releases/download/v0.9.23/diamond-linux64.tar.gz tar xzf diamond-linux64.tar.gz The extracted `diamond` binary file should be moved to a directory contained in your executable search path (PATH environment variable). To now run an alignment task, we assume to have a protein database file in FASTA format named `nr.faa` and a file of DNA reads that we want to align named `reads.fna`. In order to set up a reference database for DIAMOND, the `makedb` command needs to be executed with the following command line: $ diamond makedb --in nr.faa -d nr This will create a binary DIAMOND database file with the specified name (`nr.dmnd`). The alignment task may then be initiated using the `blastx` command like this: $ diamond blastx -d nr -q reads.fna -o matches.m8 The output file here is specified with the `–o` option and named `matches.m8`. By default, it is generated in BLAST tabular format. **Note**: - The program may use quite a lot of memory and also temporary disk space. Should the program fail due to running out of either one, you need to set a lower value for the block size parameter `-b` (see the [manual](https://github.com/bbuchfink/diamond/raw/master/diamond_manual.pdf)). - The default (fast) mode was mainly designed for short reads. For longer sequences, the sensitive modes (options `--sensitive` or `--more-sensitive`) are recommended. - The runtime of the program is not linear in the size of the query file and it is much more efficient for large query files (\> 1 million sequences) than for smaller ones. - Low complexity masking is applied to the query and reference sequences by default. Masked residues appear in the output as X. - The default e-value cutoff of DIAMOND is 0.001 while that of BLAST is 10, so by default the program will search a lot more stringently than BLAST and not report weak hits. About ===== DIAMOND is developed by Benjamin Buchfink at the Detlef Weigel lab, Max Planck Institute for Developmental Biology, Tübingen, Germany. \[[Email](mailto:buchfink@gmail.com)\] \[[Twitter](https://twitter.com/bbuchfink)\] \[[Google Scholar](https://scholar.google.de/citations?user=kjPIF1cAAAAJ)\] \[[MPI-EBIO](http://eb.tuebingen.mpg.de/)\] Publication: - Buchfink B, Xie C, Huson DH, \"Fast and sensitive protein alignment using DIAMOND\", *Nature Methods* **12**, 59-60 (2015). [doi:10.1038/nmeth.3176](https://doi.org/10.1038/nmeth.3176) Loading
.gitignore +3 −3 Original line number Diff line number Diff line Loading @@ -52,6 +52,6 @@ build/ .idea Makefile diamond src/extra/benchmark.cpp src/extra/test.cpp src/extra/seed_stat.cpp No newline at end of file src/extra/ .vs/ CMakeSettings.json
.travis.yml 0 → 100644 +8 −0 Original line number Diff line number Diff line matrix: include: - language: c++ compiler: g++ script: mkdir build; cd build; cmake ..; make - language: c++ compiler: clang script: mkdir build; cd build; cmake ..; make
CMakeLists.txt +11 −1 Original line number Diff line number Diff line Loading @@ -10,6 +10,8 @@ if(BUILD_STATIC) set(CMAKE_EXE_LINKER_FLAGS "-static") endif() set(CMAKE_CXX_STANDARD 11) if(CMAKE_BUILD_MARCH) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=${CMAKE_BUILD_MARCH}") else() Loading @@ -24,7 +26,11 @@ find_package(ZLIB REQUIRED) find_package(Threads REQUIRED) set(CMAKE_BUILD_TYPE Release) set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized -Wno-deprecated-declarations -Wno-ignored-attributes -Wno-unused-variable") if(WIN32) add_definitions(-D_CRT_SECURE_NO_WARNINGS) else() set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wno-uninitialized -Wno-ignored-attributes -Wno-unused-variable") endif() include_directories( "${CMAKE_SOURCE_DIR}/src" Loading Loading @@ -113,6 +119,10 @@ add_executable(diamond src/run/main.cpp src/util/memory/memory_pool.cpp src/data/seed_array.cpp src/output/paf_format.cpp src/util/system/system.cpp src/run/cluster.cpp src/util/algo/greedy_vortex_cover.cpp src/util/algo/greedy_vortex_cover_weighted.cpp ) if(EXTRA) Loading
LICENSE +112 −57 Original line number Diff line number Diff line GNU AFFERO GENERAL PUBLIC LICENSE Version 3, 19 November 2007 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/> Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The GNU Affero General Public License is a free, copyleft license for software and other kinds of works, specifically designed to ensure cooperation with the community in the case of network server software. The GNU General Public License is a free, copyleft license for software and other kinds of works. The licenses for most software and other practical works are designed to take away your freedom to share and change the works. By contrast, our General Public Licenses are intended to guarantee your freedom to the GNU General Public License is intended to guarantee your freedom to share and change all versions of a program--to make sure it remains free software for all its users. software for all its users. We, the Free Software Foundation, use the GNU General Public License for most of our software; it applies also to any other work released this way by its authors. You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you Loading @@ -24,34 +26,44 @@ them if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs, and that you know you can do these things. Developers that use our General Public Licenses protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License which gives you legal permission to copy, distribute and/or modify the software. A secondary benefit of defending all users' freedom is that improvements made in alternate versions of the program, if they receive widespread use, become available for other developers to incorporate. Many developers of free software are heartened and encouraged by the resulting cooperation. However, in the case of software used on network servers, this result may fail to come about. The GNU General Public License permits making a modified version and letting the public access it on a server without ever releasing its source code to the public. The GNU Affero General Public License is designed specifically to ensure that, in such cases, the modified source code becomes available to the community. It requires the operator of a network server to provide the source code of the modified version running there to the users of that server. Therefore, public use of a modified version, on a publicly accessible server, gives the public access to the source code of the modified version. An older license, called the Affero General Public License and published by Affero, was designed to accomplish similar goals. This is a different license, not a version of the Affero GPL, but Affero has released a new version of the Affero GPL which permits relicensing under this license. To protect your rights, we need to prevent others from denying you these rights or asking you to surrender the rights. Therefore, you have certain responsibilities if you distribute copies of the software, or if you modify it: responsibilities to respect the freedom of others. For example, if you distribute copies of such a program, whether gratis or for a fee, you must pass on to the recipients the same freedoms that you received. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. Developers that use the GNU GPL protect your rights with two steps: (1) assert copyright on the software, and (2) offer you this License giving you legal permission to copy, distribute and/or modify it. For the developers' and authors' protection, the GPL clearly explains that there is no warranty for this free software. For both users' and authors' sake, the GPL requires that modified versions be marked as changed, so that their problems will not be attributed erroneously to authors of previous versions. Some devices are designed to deny users access to install or run modified versions of the software inside them, although the manufacturer can do so. This is fundamentally incompatible with the aim of protecting users' freedom to change the software. The systematic pattern of such abuse occurs in the area of products for individuals to use, which is precisely where it is most unacceptable. Therefore, we have designed this version of the GPL to prohibit the practice for those products. If such problems arise substantially in other domains, we stand ready to extend this provision to those domains in future versions of the GPL, as needed to protect the freedom of users. Finally, every program is threatened constantly by software patents. States should not allow patents to restrict development and use of software on general-purpose computers, but in those that do, we wish to avoid the special danger that patents applied to a free program could make it effectively proprietary. To prevent this, the GPL assures that patents cannot be used to render the program non-free. The precise terms and conditions for copying, distribution and modification follow. Loading @@ -60,7 +72,7 @@ modification follow. 0. Definitions. "This License" refers to version 3 of the GNU Affero General Public License. "This License" refers to version 3 of the GNU General Public License. "Copyright" also means copyright-like laws that apply to other kinds of works, such as semiconductor masks. Loading Loading @@ -537,45 +549,35 @@ to collect a royalty for further conveying from those to whom you convey the Program, the only way you could satisfy both those terms and this License would be to refrain entirely from conveying the Program. 13. Remote Network Interaction; Use with the GNU General Public License. Notwithstanding any other provision of this License, if you modify the Program, your modified version must prominently offer all users interacting with it remotely through a computer network (if your version supports such interaction) an opportunity to receive the Corresponding Source of your version by providing access to the Corresponding Source from a network server at no charge, through some standard or customary means of facilitating copying of software. This Corresponding Source shall include the Corresponding Source for any work covered by version 3 of the GNU General Public License that is incorporated pursuant to the following paragraph. 13. Use with the GNU Affero General Public License. Notwithstanding any other provision of this License, you have permission to link or combine any covered work with a work licensed under version 3 of the GNU General Public License into a single under version 3 of the GNU Affero General Public License into a single combined work, and to convey the resulting work. The terms of this License will continue to apply to the part which is the covered work, but the work with which it is combined will remain governed by version 3 of the GNU General Public License. but the special requirements of the GNU Affero General Public License, section 13, concerning interaction through a network will apply to the combination as such. 14. Revised Versions of this License. The Free Software Foundation may publish revised and/or new versions of the GNU Affero General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to the GNU General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies that a certain numbered version of the GNU Affero General Program specifies that a certain numbered version of the GNU General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that numbered version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of the GNU Affero General Public License, you may choose any version ever published GNU General Public License, you may choose any version ever published by the Free Software Foundation. If the Program specifies that a proxy can decide which future versions of the GNU Affero General Public License can be used, that proxy's versions of the GNU General Public License can be used, that proxy's public statement of acceptance of a version permanently authorizes you to choose that version for the Program. Loading Loading @@ -617,3 +619,56 @@ Program, unless a warranty or assumption of liability accompanies a copy of the Program in return for a fee. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. <one line to give the program's name and a brief idea of what it does.> Copyright (C) <year> <name of author> This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <https://www.gnu.org/licenses/>. Also add information on how to contact you by electronic and paper mail. If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode: <program> Copyright (C) <year> <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, your program's commands might be different; for a GUI interface, you would use an "about box". You should also get your employer (if you work as a programmer) or school, if any, to sign a "copyright disclaimer" for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see <https://www.gnu.org/licenses/>. The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read <https://www.gnu.org/licenses/why-not-lgpl.html>.
README.md 0 → 100644 +92 −0 Original line number Diff line number Diff line Introduction ============ DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are: - Pairwise alignment of proteins and translated DNA at 500x-20,000x speed of BLAST. - Frameshift alignments for long read analysis. - Low resource requirements and suitable for running on standard desktops or laptops. - Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification. Keep posted about new developments by following me on [Twitter](https://twitter.com/bbuchfink). [](https://travis-ci.org/bbuchfink/diamond) [](https://anaconda.org/bioconda/diamond)  [](https://anaconda.org/bioconda/diamond) Quick start guide ================= Please read the [manual](https://github.com/bbuchfink/diamond/raw/master/diamond_manual.pdf) for detailed installation and usage instructions. This demonstrates a quick example for setting up and using the program on Linux. Installing the software on your system may be done by downloading it in binary format for immediate use: wget http://github.com/bbuchfink/diamond/releases/download/v0.9.23/diamond-linux64.tar.gz tar xzf diamond-linux64.tar.gz The extracted `diamond` binary file should be moved to a directory contained in your executable search path (PATH environment variable). To now run an alignment task, we assume to have a protein database file in FASTA format named `nr.faa` and a file of DNA reads that we want to align named `reads.fna`. In order to set up a reference database for DIAMOND, the `makedb` command needs to be executed with the following command line: $ diamond makedb --in nr.faa -d nr This will create a binary DIAMOND database file with the specified name (`nr.dmnd`). The alignment task may then be initiated using the `blastx` command like this: $ diamond blastx -d nr -q reads.fna -o matches.m8 The output file here is specified with the `–o` option and named `matches.m8`. By default, it is generated in BLAST tabular format. **Note**: - The program may use quite a lot of memory and also temporary disk space. Should the program fail due to running out of either one, you need to set a lower value for the block size parameter `-b` (see the [manual](https://github.com/bbuchfink/diamond/raw/master/diamond_manual.pdf)). - The default (fast) mode was mainly designed for short reads. For longer sequences, the sensitive modes (options `--sensitive` or `--more-sensitive`) are recommended. - The runtime of the program is not linear in the size of the query file and it is much more efficient for large query files (\> 1 million sequences) than for smaller ones. - Low complexity masking is applied to the query and reference sequences by default. Masked residues appear in the output as X. - The default e-value cutoff of DIAMOND is 0.001 while that of BLAST is 10, so by default the program will search a lot more stringently than BLAST and not report weak hits. About ===== DIAMOND is developed by Benjamin Buchfink at the Detlef Weigel lab, Max Planck Institute for Developmental Biology, Tübingen, Germany. \[[Email](mailto:buchfink@gmail.com)\] \[[Twitter](https://twitter.com/bbuchfink)\] \[[Google Scholar](https://scholar.google.de/citations?user=kjPIF1cAAAAJ)\] \[[MPI-EBIO](http://eb.tuebingen.mpg.de/)\] Publication: - Buchfink B, Xie C, Huson DH, \"Fast and sensitive protein alignment using DIAMOND\", *Nature Methods* **12**, 59-60 (2015). [doi:10.1038/nmeth.3176](https://doi.org/10.1038/nmeth.3176)
