### Log Installation Paths

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/build/cmake/CMakeLists.txt

Logs the installation prefix and library directory paths. This is useful for debugging installation issues.

```cmake
MESSAGE(STATUS "CMAKE_INSTALL_PREFIX: ${CMAKE_INSTALL_PREFIX}")
MESSAGE(STATUS "CMAKE_INSTALL_LIBDIR: ${CMAKE_INSTALL_LIBDIR}")
```

--------------------------------

### Build and Install zstd-adaptive

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/contrib/adaptive-compression/README.md

Build the adaptive compression tool by running 'make adapt' in the specified directory. For system-wide installation, use 'make install' to create the 'zstd-adaptive' command.

```bash
make adapt
make install
```

--------------------------------

### Install Zstandard to Staging Directory

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/build/meson/README.md

Install the zstandard library into a staging directory using DESTDIR with ninja.

```sh
DESTDIR=./staging ninja install
```

--------------------------------

### Global Alignment with KSW2 Library

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/ksw2/README.md

This example demonstrates how to perform a global alignment using the ksw_extz function from the KSW2 library. It includes sequence encoding, scoring matrix setup, and CIGAR string generation. Ensure ksw2.h is included and the relevant ksw2_*.c file is compiled.

```c
#include <string.h>
#include <stdio.h>
#include "ksw2.h"

void align(const char *tseq, const char *qseq, int sc_mch, int sc_mis, int gapo, int gape)
{
	int i, a = sc_mch, b = sc_mis < 0? sc_mis : -sc_mis; // a>0 and b<0
	int8_t mat[25] = { a,b,b,b,0, b,a,b,b,0, b,b,a,b,0, b,b,b,a,0, 0,0,0,0,0 };
	int tl = strlen(tseq), ql = strlen(qseq);
	uint8_t *ts, *qs, c[256];
	ksw_extz_t ez;

	memset(&ez, 0, sizeof(ksw_extz_t));
	memset(c, 4, 256);
	c['A'] = c['a'] = 0; c['C'] = c['c'] = 1;
	c['G'] = c['g'] = 2; c['T'] = c['t'] = 3; // build the encoding table
	ts = (uint8_t*)malloc(tl);
	qs = (uint8_t*)malloc(ql);
	for (i = 0; i < tl; ++i) ts[i] = c[(uint8_t)tseq[i]]; // encode to 0/1/2/3
	for (i = 0; i < ql; ++i) qs[i] = c[(uint8_t)qseq[i]];
	ksw_extz(0, ql, qs, tl, ts, 5, mat, gapo, gape, -1, -1, 0, &ez);
	for (i = 0; i < ez.n_cigar; ++i) // print CIGAR
		printf("%d%c", ez.cigar[i]>>4, "MID"[ez.cigar[i]&0xf]);
	putchar('\n');
	free(ez.cigar); free(ts); free(qs);
}

int main(int argc, char *argv[])
{
	align("ATAGCTAGCTAGCAT", "AGCTAcCGCAT", 1, -2, 2, 1);
	return 0;
}

```

--------------------------------

### Install Corrosion from Source

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/corrosion/doc/src/setup_corrosion.md

Build and install Corrosion from its source code. This process includes pre-building native tooling for older CMake versions. Ensure the installation directory is in your PATH or CMAKE_PREFIX_PATH.

```bash
git clone https://github.com/corrosion-rs/corrosion.git
# Optionally, specify -DCMAKE_INSTALL_PREFIX=<target-install-path> to specify a 
# custom installation directory
cmake -Scorrosion -Bbuild -DCMAKE_BUILD_TYPE=Release
cmake --build build --config Release
# This next step may require sudo or admin privileges if you're installing to a system location,
# which is the default.
cmake --install build --config Release
```

--------------------------------

### Install cross-compiler for PowerPC on Ubuntu

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/corrosion/doc/src/usage.md

Install the necessary g++ cross-compiler for 64-bit Little-Endian PowerPC on Ubuntu using apt-get.

```bash
sudo apt install g++-powerpc64le-linux-gnu
```

--------------------------------

### Get Module Help

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Call any MMseqs2 module without arguments to get a short description, usage text, and a list of important options.

```bash
mmseqs createdb
```

--------------------------------

### PZstandard Piping Example

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/contrib/pzstd/README.md

Demonstrates using PZstandard with standard input/output streams for compression, piping data to /dev/null.

```bash
cat input-file | pzstd -p num-threads -# -c > /dev/null
```

--------------------------------

### Print Hello World to Stdout

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/fmt/README.md

Basic example of printing a simple string to standard output using fmt::print.

```c++
#include <fmt/core.h>

int main() {
  fmt::print("Hello, world!\n");
}
```

--------------------------------

### Example compilation with zstd wrapper

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/zlibWrapper/README.md

Compile the example.c file with the zstd wrapper enabled and link with the zstd library.

```bash
gcc example.c zstd_zlibwrapper.o gz*.c -DZWRAP_USE_ZSTD=1 -lzstd
```

--------------------------------

### Basic CMake Project Setup

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/corrosion/test/cpp2rust/cpp2rust/CMakeLists.txt

Sets the minimum CMake version and defines the project name and version.

```cmake
cmake_minimum_required(VERSION 3.15)
project(test_project VERSION 0.1.0)
```

--------------------------------

### Install Rust Target Standard Library for Cross-Compiling

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/corrosion/doc/src/usage.md

When cross-compiling Rust code, you must install the standard library for the target triple. Use `rustup target add` to install the necessary components for the specified Rust target.

```bash
rustup target add <target-rust-triple>
```

--------------------------------

### Run Nanopore Bench Global Example

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/block-aligner/vis/block_aligner_bench_vis.ipynb

Executes the nanopore_bench_global example using cargo, enabling AVX2 features for performance. The output captures the benchmark results.

```python
output = !cd .. && cargo run --example nanopore_bench_global --release --features simd_avx2 --quiet
output
```

--------------------------------

### Build makedb

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/libmarv/Readme.md

Compiles the 'makedb' component of the software. Ensure you have the necessary software requirements installed.

```bash
make makedb
```

--------------------------------

### Printf Formatting Example

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/fmt/README.md

Shows the conciseness of printf for formatting floating-point numbers.

```c++
printf("%.2f\n", 1.23456);
```

--------------------------------

### Install Static Zstd Library

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/build/cmake/lib/CMakeLists.txt

Installs the static Zstd library to the archive destination.

```cmake
IF (ZSTD_BUILD_STATIC)
    INSTALL(TARGETS libzstd_static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}")
ENDIF (ZSTD_BUILD_STATIC)
```

--------------------------------

### Install MMseqs2 via Homebrew

Source: https://github.com/soedinglab/mmseqs2/blob/master/README.md

Use this command to install MMseqs2 if you are using Homebrew as your package manager.

```bash
brew install mmseqs2
```

--------------------------------

### Install Zstd Headers

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/build/cmake/lib/CMakeLists.txt

Installs the Zstd header files to the include directory.

```cmake
INSTALL(FILES
    ${LIBRARY_DIR}/zstd.h
    ${LIBRARY_DIR}/deprecated/zbuff.h
    ${LIBRARY_DIR}/dictBuilder/zdict.h
    ${LIBRARY_DIR}/dictBuilder/cover.h
    ${LIBRARY_DIR}/common/zstd_errors.h
    DESTINATION "include")
```

--------------------------------

### Include GNU Install Directories

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/build/cmake/CMakeLists.txt

Includes standard CMake modules for defining installation directories according to GNU standards.

```cmake
INCLUDE(GNUInstallDirs)
```

--------------------------------

### Run Nanopore Accuracy Example

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/block-aligner/vis/block_aligner_accuracy_vis.ipynb

Executes the nanopore_accuracy example using cargo, enabling AVX2 features for performance. The output is captured for further processing.

```python
output = !cd .. && cargo run --example nanopore_accuracy --release --features simd_avx2 --quiet
output
```

--------------------------------

### Install MMseqs2 via Docker

Source: https://github.com/soedinglab/mmseqs2/blob/master/README.md

Pull the official MMseqs2 Docker image from GitHub Container Registry.

```bash
docker pull ghcr.io/soedinglab/mmseqs2
```

--------------------------------

### Download and Install MMseqs2 Static SSE4.1 Binary

Source: https://github.com/soedinglab/mmseqs2/blob/master/README.md

Download the static build of MMseqs2 with SSE4.1 support, extract it, and add its bin directory to your PATH.

```bash
wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz; tar xvfz mmseqs-linux-sse41.tar.gz; export PATH=$(pwd)/mmseqs/bin/:$PATH
```

--------------------------------

### Example Usage of Fake Prefiltering

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Demonstrates how to use the `fake_pref` function to set up and perform an all-vs-all alignment, followed by converting the results.

```bash
fake_pref qdb tdb allvsallpref
mmseqs align qdb tdb allvsallpref allvsallaln
mmseqs convertalis qdb tdb allvsallaln allvsall.m8
```

--------------------------------

### Create and Index Database

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Sets up a database by creating it, indexing it, and then loading the index into memory for faster access.

```bash
mmseqs createdb targetDB.fasta targetDB
mmseqs createindex targetDB tmp
mmseqs touchdb targetDB
# alternative using vmtouch
vmtouch -l -d -t targetDB.idx
```

--------------------------------

### Download Tutorial Data

Source: https://github.com/soedinglab/mmseqs2/wiki/Tutorials

Download the necessary FASTA file for the tutorial reads and the Swiss-Prot protein database with its mapping file.

```bash
wget http://wwwuser.gwdg.de/~compbiol/mmseqs2/tutorials/mystery_reads.fasta
```

```bash
wget http://wwwuser.gwdg.de/~compbiol/mmseqs2/tutorials/uniprot_sprot_2018_03.fasta.gz
```

```bash
wget http://wwwuser.gwdg.de/~compbiol/mmseqs2/tutorials/uniprot_sprot_2018_03_mapping.tsv.gz
```

```bash
gunzip uniprot_sprot_2018_03_mapping.tsv.gz
```

--------------------------------

### Download and Setup Swiss-Prot Database

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Use the 'databases' command to download and prepare specific databases like UniProtKB/Swiss-Prot. Specify the database name, output path, and a temporary directory. This prepares the database for use as a seqTaxDB if taxonomy information is available.

```bash
mmseqs databases UniProtKB/Swiss-Prot outpath/swissprot tmp
```

--------------------------------

### Install Corrosion for Testing

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/corrosion/test/CMakeLists.txt

Configures tests to install Corrosion to a specific test directory and then use the installed version.

```cmake
option(CORROSION_TESTS_INSTALL_CORROSION
        "Install Corrosion to a test directory and let tests use the installed Corrosion"
        OFF)
if(CORROSION_TESTS_INSTALL_CORROSION)
    add_test(NAME "install_corrosion_configure"
        COMMAND
            ${CMAKE_COMMAND}
            -S "${CMAKE_CURRENT_SOURCE_DIR}/.."
            -B "${CMAKE_CURRENT_BINARY_DIR}/build-corrosion"
            -DCORROSION_VERBOSE_OUTPUT=ON
            -DCORROSION_TESTS=OFF
            -DCMAKE_BUILD_TYPE=Release
            -G${CMAKE_GENERATOR}
            "-DCMAKE_INSTALL_PREFIX=${test_install_path}"
    )
    add_test(NAME "install_corrosion_build"
            COMMAND
            ${CMAKE_COMMAND} --build "${CMAKE_CURRENT_BINARY_DIR}/build-corrosion" --config Release
            )
    add_test(NAME "install_corrosion_install"
            COMMAND
            ${CMAKE_COMMAND} --install "${CMAKE_CURRENT_BINARY_DIR}/build-corrosion" --config Release
        )
    set_tests_properties("install_corrosion_configure" PROPERTIES FIXTURES_SETUP "fixture_corrosion_configure")
    set_tests_properties("install_corrosion_build"     PROPERTIES FIXTURES_SETUP "fixture_corrosion_build")
    set_tests_properties("install_corrosion_build"     PROPERTIES FIXTURES_REQUIRED "fixture_corrosion_configure")
    set_tests_properties("install_corrosion_install"   PROPERTIES FIXTURES_REQUIRED "fixture_corrosion_build")
    set_tests_properties("install_corrosion_install"   PROPERTIES FIXTURES_SETUP "fixture_corrosion_install")

    add_test(NAME "install_corrosion_build_cleanup" COMMAND "${CMAKE_COMMAND}" -E remove_directory "${CMAKE_CURRENT_BINARY_DIR}/build-corrosion")
    set_tests_properties("install_corrosion_build_cleanup" PROPERTIES
        FIXTURES_CLEANUP
        "fixture_corrosion_configure;fixture_corrosion_build"
    )

    add_test(NAME "install_corrosion_cleanup" COMMAND "${CMAKE_COMMAND}" -E remove_directory "${test_install_path}")
    set_tests_properties("install_corrosion_cleanup" PROPERTIES
        FIXTURES_CLEANUP
        "fixture_corrosion_configure;fixture_corrosion_build;fixture_corrosion_install"
    )
endif()
```

--------------------------------

### Run MMseqs2 Docker Container with Mounted Volume

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Example of running the MMseqs2 Docker container, mounting the current directory, and executing a command.

```shell
docker run -v "$(pwd):/app" ghcr.io/soedinglab/mmseqs2 easy-search /app/QUERY.fasta /app/DB.fasta /app/result.m8 /app/tmp
```

--------------------------------

### Build and Run PZstandard Tests

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/contrib/pzstd/README.md

Commands to build and run tests for PZstandard, assuming gtest is installed or built via make.

```bash
make tests && make check
```

--------------------------------

### Executing Cargo Install for Generator Build

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/corrosion/generator/CMakeLists.txt

Installs the Corrosion generator using cargo install, specifying the Rust compiler and output directory. Handles potential build failures.

```cmake
execute_process(
        COMMAND ${CMAKE_COMMAND}
        -E env
        # If the Generator is built at configure of a project (instead of being pre-installed)
        # We don't want environment variables like `RUSTFLAGS` affecting the Generator build.
        --unset=RUSTFLAGS
        "CARGO_BUILD_RUSTC=${RUSTC_EXECUTABLE}"
        "${CARGO_EXECUTABLE}" install
        --path "."
        --root "${generator_destination}"
        --locked
        ${_CORROSION_QUIET_OUTPUT_FLAG}
        WORKING_DIRECTORY "${generator_src}"
        RESULT_VARIABLE generator_build_failed
)
if(generator_build_failed)
    message(FATAL_ERROR "Building CMake Generator for Corrosion - failed")
else()
    message(STATUS "Building CMake Generator for Corrosion - done")
endif()
```

--------------------------------

### Install MMseqs2 and related tools with Conda

Source: https://github.com/soedinglab/mmseqs2/wiki/Tutorials

Sets up a Conda environment named 'tutorial' with MMseqs2, Plass, and other necessary bioinformatics tools. Activate the environment before running commands.

```bash
conda create -n tutorial -c conda-forge -c bioconda mmseqs2 plass megahit prodigal hmmer sra-tools
conda activate tutorial
```

--------------------------------

### Install Shared Zstd Library

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/build/cmake/lib/CMakeLists.txt

Installs the shared Zstd library to runtime, library, and archive destinations.

```cmake
IF (ZSTD_BUILD_SHARED)
    INSTALL(TARGETS libzstd_shared RUNTIME DESTINATION "bin"
                                   LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
                                   ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}")
ENDIF()
```

--------------------------------

### Compile MMseqs2 from Source on Linux

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Clones the MMseqs2 repository, builds it from source using CMake and Make, and installs it. Optimizes performance for the specific system.

```bash
git clone https://github.com/soedinglab/MMseqs2.git
cd MMseqs2
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=RELEASE -DCMAKE_INSTALL_PREFIX=. ..
make -j8
make install 
export PATH=$(pwd)/bin/:$PATH
```

--------------------------------

### List Available Databases

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Run 'mmseqs databases' without parameters to view a list of prepared databases, their types, taxonomy information, and download URLs. Use '-h' for extended descriptions.

```bash
# mmseqs databases
Usage: mmseqs databases <name> <o:sequenceDB> <tmpDir> [options]

  Name                	Type      	Taxonomy	Url
- UniRef100           	Aminoacid 	     yes	https://www.uniprot.org/help/uniref
- UniRef90            	Aminoacid 	     yes	https://www.uniprot.org/help/uniref
- UniRef50            	Aminoacid 	     yes	https://www.uniprot.org/help/uniref
- UniProtKB           	Aminoacid 	     yes	https://www.uniprot.org/help/uniprotkb
- UniProtKB/TrEMBL    	Aminoacid 	     yes	https://www.uniprot.org/help/uniprotkb
- UniProtKB/Swiss-Prot	Aminoacid 	     yes	https://www.uniprot.org
- NR                  	Aminoacid 	     yes	https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA
- NT                  	Nucleotide	       -	https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA
- GTDB                Aminoacid	     yes	https://gtdb.ecogenomic.org
- PDB                 	Aminoacid 	       -	https://www.rcsb.org
- PDB70               	Profile   	       -	https://github.com/soedinglab/hh-suite
- Pfam-A.full         	Profile   	       -	https://pfam.xfam.org
- Pfam-A.seed         	Profile   	       -	https://pfam.xfam.org
- Pfam-B              	Profile   	       -	https://xfam.wordpress.com/2020/06/30/a-new-pfam-b-is-released
- CDD                   Profile                -	https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
- eggNOG              	Profile   	       -	http://eggnog5.embl.de
- VOGDB                 Profile                -	https://vogdb.org
- dbCAN2              	Profile   	       -	http://bcb.unl.edu/dbCAN2
- SILVA                 Nucleotide           yes	https://www.arb-silva.de
- Resfinder           	Nucleotide	       -	https://cge.cbs.dtu.dk/services/ResFinder
- Kalamari            	Nucleotide	     yes	https://github.com/lskatz/Kalamari
```

--------------------------------

### Install MMseqs2 via Conda

Source: https://github.com/soedinglab/mmseqs2/blob/master/README.md

Install MMseqs2 using conda, specifying the conda-forge and bioconda channels.

```bash
conda install -c conda-forge -c bioconda mmseqs2
```

--------------------------------

### Basic TinyExpr Library Build

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/tinyexpr/CMakeLists.txt

Configures and builds the static TinyExpr C library. It sets compiler flags and installs the library and header files.

```cmake
cmake_minimum_required(VERSION 3.15)
project(tinyexpr C)

option(TE_POW_FROM_RIGHT "Evaluate exponents from right to left." OFF)
option(TE_NAT_LOG "Define the log function as natural logarithm." OFF)
option(build_tinyexpr_test "Build TinyExpr tests." OFF)
option(build_tinyexpr_test_pr "Build TinyExpr tests PR." OFF)
option(build_tinyexpr_bench "Build TinyExpr benchmark." OFF)
option(build_tinyexpr_example "Build TinyExpr example." OFF)
option(build_tinyexpr_example2 "Build TinyExpr example 2." OFF)
option(build_tinyexpr_example3 "Build TinyExpr example 3." OFF)

set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -ansi -Wall -Wshadow -fPIC -O3")

set(SOURCE_FILES
        tinyexpr.c
        tinyexpr.h
        )

add_library(tinyexpr STATIC ${SOURCE_FILES})
set_target_properties(tinyexpr PROPERTIES COMPILE_FLAGS "${MMSEQS_C_FLAGS}" LINK_FLAGS "${MMSEQS_C_FLAGS}")
if (TE_POW_FROM_RIGHT)
    target_compile_definitions(tinyexpr PRIVATE TE_POW_FROM_RIGHT)
endif()
if (TE_NAT_LOG)
    target_compile_definitions(tinyexpr PRIVATE TE_NAT_LOG)
endif()
install(TARGETS tinyexpr ARCHIVE DESTINATION lib)
install(FILES tinyexpr.h DESTINATION include COMPONENT Devel)
```

--------------------------------

### Clone and Build Format Benchmarks

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/fmt/README.md

Clone the format-benchmark repository and configure it with CMake to prepare for running benchmarks.

```bash
git clone --recursive https://github.com/fmtlib/format-benchmark.git
cd format-benchmark
cmake .
```

--------------------------------

### Prepare Swiss-Prot Reference Database

Source: https://github.com/soedinglab/mmseqs2/wiki/Tutorials

Create an MMseqs2 sequence database and a taxonomic database from the downloaded Swiss-Prot data.

```bash
mmseqs createdb uniprot_sprot_2018_03.fasta.gz uniprot_sprot
```

```bash
mmseqs createtaxdb uniprot_sprot tmp --tax-mapping-file uniprot_sprot_2018_03_mapping.tsv
```

--------------------------------

### Find Installed Corrosion Package

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/corrosion/doc/src/setup_corrosion.md

After installing Corrosion and ensuring it's in your PATH, find and use it in your CMakeLists.txt.

```cmake
find_package(Corrosion REQUIRED)
```

--------------------------------

### Create Sequence Database and Initial Clustering

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Creates a sequence database from a trimmed FASTA file and performs an initial clustering. This sets up the database that will be updated later.

```bash
mmseqs createdb DB_trimmed.fasta DB_trimmed
mmseqs cluster DB_trimmed DB_trimmed_clu tmp
```

--------------------------------

### Example LCA output

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Example of the resulting TSV file containing taxonomic assignments for each set representative.

```tsv
A7ZUJ8	91347	order	Enterobacterales

```

--------------------------------

### Create Profile Database

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Use this command to initialize an empty MMseqs2 database file for profiles.

```bash
awk 'BEGIN { printf("%c%c%c%c",2,0,0,0); exit; }' > seqDb.dbtype
```

--------------------------------

### MMseqs2 Database Example Data

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Example data file content for an MMseqs2 database containing four sequences.

```text
PSSLDIRL
\0GTLKRLSAHYTPAW
\0AEAIFIHEG
\0YTHGAGFDNDI
\0
```

--------------------------------

### Install Corrosion via Homebrew

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/corrosion/doc/src/setup_corrosion.md

Install Corrosion using the Homebrew package manager. Note that this is an unofficial, community-maintained package.

```bash
brew install corrosion
```

--------------------------------

### MMseqs2 Database Example Index

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Example index file content corresponding to the MMseqs2 database data, showing IDs, offsets, and sizes.

```text
10  0   9
11  9  15  
12  24  10
13  34  12

```

--------------------------------

### Create MMseqs2 sequence and taxonomy databases

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Commands to create a sequence database and a taxonomy database from input files.

```bash
mmseqs createdb sequences.fasta seqdb
mmseqs createtaxdb seqdb tmp --tax-mapping-file taxonomy.tsv

```

--------------------------------

### ZSTD CLI Usage Example

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/lib/dll/example/README.md

Shows the basic usage syntax for the ZSTD command-line interface. Use -h or -H for a full list of commands.

```bash
    Usage: zstd [arg] [input] [output]
```

--------------------------------

### Converted Alignment Results Example

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Shows an example of alignment results converted into a flat file format, potentially using tools like createtsv or convertalis.

```text
Q0KJ32	Q0KJ32	783	1.000	7.540E-260	0	418	419	0	418	419	419M
Q0KJ32	C0W539	260	0.455	1.305E-79	26	368	379	21	363	369	173M2D41M2D65M6I21M2D37M
Q0KJ32	D6KVP9	233	0.434	2.830E-70	25	364	379	30	367	373	162M2I16M3I10M1I5M6D16M2D67M6I25M2D27M
```

--------------------------------

### Download and Install MMseqs2 Static AVX2 Binary

Source: https://github.com/soedinglab/mmseqs2/blob/master/README.md

Download the fastest static build of MMseqs2 with AVX2 support, extract it, and add its bin directory to your PATH.

```bash
wget https://mmseqs.com/latest/mmseqs-linux-avx2.tar.gz; tar xvfz mmseqs-linux-avx2.tar.gz; export PATH=$(pwd)/mmseqs/bin/:$PATH
```

--------------------------------

### Example Taxonomy Classification Output

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

This is an example of the taxonomy classification output produced by the 'lca' module, showing a numeric identifier, rank, and name for two sequences.

```text
1758121 subspecies      Limosa lapponica baueri
	0       no rank unclassified
```

--------------------------------

### Configure and Build Zstandard with Meson

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/build/meson/README.md

Configure the zstandard build with specific options like build type, enabling contributions, and tests. Then, build the project using ninja.

```sh
meson --buildtype=release -D with-contrib=true -D with-tests=true -D with-contrib=true builddir
cd builddir
ninja             # to build
ninja install     # to install
```

--------------------------------

### Run Block Aligner Accuracy Example

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/block-aligner/vis/block_aligner_accuracy_vis.ipynb

Executes the `uc_accuracy` example using MMseqs2's cargo, enabling SIMD acceleration. The output is captured for further processing.

```python
output = !cd .. && cargo run --example uc_accuracy --release --features simd_avx2 --quiet
output
```

--------------------------------

### Create index for expandable profile database

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Builds an index for a precomputed profile database to speed up searches. Requires sufficient RAM.

```bash
mmseqs createindex uniref30_2103_db tmp --split 1
```

--------------------------------

### Example Kraken-style Taxonomy Report Output

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

An example of the output format for a Kraken-style taxonomy report, showing clade percentages, read counts, rank, and scientific names.

```text
5.6829  362     362       no rank       0  unclassified
94.3171 6008    43        no rank       1  root
87.8493 5596    126       no rank  131567    cellular organisms
42.5903 2713    79   superkingdom    2759      Eukaryota
32.8257 2091    38        no rank   33154        Opisthokonta
24.0502 1532    2         kingdom   33208          Metazoa
23.8776 1521    3         no rank    6072            Eumetazoa
23.2810 1483    49        no rank   33213              Bilateria
14.2857 910     2         no rank   33511                Deuterostomia
13.9560 889     3          phylum    7711                  Chordata
13.3124 848     0       subphylum   89593                     Craniata  
```

--------------------------------

### Initialize ZSTD Compression Context with Advanced Parameters

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/doc/zstd_manual.html

Initializes a ZSTD compression context with advanced parameters, including dictionary, ZSTD_parameters, and pledged source size. Use this for fine-grained control over compression.

```c
size_t ZSTD_compressBegin_advanced(ZSTD_CCtx* cctx, const void* dict, size_t dictSize, ZSTD_parameters params, unsigned long long pledgedSrcSize);
```

--------------------------------

### Run PSSM Accuracy Example

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/block-aligner/vis/block_aligner_accuracy_vis.ipynb

Executes the 'pssm_accuracy' example from the Rust project using Cargo, enabling AVX2 SIMD instructions and running quietly. The output is captured.

```bash
output = !cd .. && cargo run --example pssm_accuracy --release --features simd_avx2 --quiet
output
```

--------------------------------

### Install Dependencies for Compiling MMseqs2 with Clang (macOS)

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Installs necessary build tools and libraries (CMake, libomp, zlib, bzip2) for compiling MMseqs2 with Clang on macOS using Homebrew.

```bash
brew install cmake libomp zlib bzip2
```

--------------------------------

### Build Zstandard with Makefile

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/README.md

Generates the zstd CLI in the root directory by invoking 'make' in the project's root directory. Supports 'make install' and 'make check' for installation and testing.

```bash
make
```

--------------------------------

### PZstandard Help Command

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/contrib/pzstd/README.md

Displays the help message for PZstandard, showing all available options and usage information.

```bash
pzstd --help
```

--------------------------------

### Example Taxonomy Top Hit Report Output

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

An example of a taxonomy top hit report, detailing target identifier, alignment counts, coverage, sequence identity, and taxonomic information.

```text
A0A6B9SVR4 6 0.744 1.026 0.419 112596 species Wolbachia phage WO d_Viruses;-_Duplodnaviria;-_Heunggongvirae;p_Uroviricota;c_Caudoviricetes;o_Caudovirales;f_Myoviridae;-_unclassified Myoviridae;s_Wolbachia phage WO
```

--------------------------------

### ZSTD_isFrame

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/doc/zstd_manual.html

Checks if the provided buffer starts with a valid Zstandard frame identifier. It considers legacy and skippable frame identifiers. Returns 0 if the buffer is too small or does not start with a valid identifier.

```APIDOC
## ZSTD_isFrame

### Description
Determines if the beginning of a given buffer contains a valid Zstandard frame identifier. This function is useful for identifying Zstandard compressed data streams.

### Parameters
- **buffer** (const void*) - Pointer to the buffer to check.
- **size** (size_t) - The size of the buffer.

### Returns
- unsigned - Returns 1 if the buffer starts with a valid frame identifier, 0 otherwise. Note that legacy frame identifiers are only considered valid if legacy support is enabled.
```

--------------------------------

### Database Construction

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/libmarv/Readme.md

Constructs a database from a FASTA file using the 'makedb' tool. The input file can be gzipped and supports up to 2 billion sequences. Ensure the output directory exists.

```bash
mkdir -p dbfolder
./makedb input.fa(.gz) dbfolder/dbname [options]
```

--------------------------------

### Install Dependencies for Compiling MMseqs2 with GCC (macOS)

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Installs necessary build tools and libraries (CMake, GCC 12, zlib, bzip2) for compiling MMseqs2 with GCC on macOS using Homebrew.

```bash
brew install cmake gcc@12 zlib bzip2
```

--------------------------------

### Initialize Compression Context Parameters with Advanced Parameters

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/doc/zstd_manual.html

Initializes compression and frame parameters using a ZSTD_parameters structure. All other parameters are reset to their default values.

```c
size_t ZSTD_CCtxParams_init_advanced(ZSTD_CCtx_params* cctxParams, ZSTD_parameters params);
```

--------------------------------

### Start and Stop MMseqs2 GPU Server

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Starts the MMseqs2 GPU server in the background and then stops it using its PID. Ensure that the same --max-seqs and --prefilter-mode parameters, along with CUDA_VISIBLE_DEVICES, are used for both gpuserver and search.

```bash
mmseqs gpuserver targetDB_gpu &
PID=$!
mmseqs search queryDB targetDB_gpu resultDB tmp --gpu 1 --gpu-server 1 --db-load-mode 2
kill $PID
```

--------------------------------

### Compiling and Generating Zstandard Manual

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/contrib/gen_html/README.md

Demonstrates the steps to compile the gen_html program using 'make' and then execute it to generate the zstd manual HTML file.

```bash
make
./gen_html.exe 1.1.1 ../../lib/zstd.h zstd_manual.html
```

--------------------------------

### Build All with Visual Studio 2015

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/build/VS_scripts/README.md

Executes the build for both Release Win32 and Release x64 versions using Visual Studio 2015.

```batch
build.VS2015.cmd
```

--------------------------------

### Example Contig Taxonomy Assignment Output

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Example output from the 'aggregatetax' module for nucleotide-protein searches. It includes query accession, taxid, rank name, fragment counts (retained, assigned, in agreement), support, and lineage information.

```text
NC_001133.9     4932    species Saccharomyces cerevisiae        32      32      30      0.890   131567;2759;33154;4751;451864;4890;716545;147537;4891;4892;4893;4930;4932
```

--------------------------------

### Parse GET Options from URL

Source: https://github.com/soedinglab/mmseqs2/blob/master/data/resources/krona_prelude.html

Parses GET parameters from the URL to configure visualization options such as collapse, color, dataset, depth, keys, font size, and node selection. Default values are set if parameters are not present.

```javascript
var datasetDefault = 0; var maxDepthDefault; var nodeDefault = 0; if ( urlHalves[1] ) { var vars = urlHalves[1].split('&'); for ( i = 0; i < vars.length; i++ ) { var pair = vars[i].split('='); switch ( pair[0] ) { case 'collapse': collapse = pair[1] == 'true'; break; case 'color': hueDefault = pair[1] == 'true'; break; case 'dataset': datasetDefault = Number(pair[1]); break; case 'depth': maxDepthDefault = Number(pair[1]) + 1; break; case 'key': showKeys = pair[1] == 'true'; break; case 'font': fontSize = Number(pair[1]); break; case 'node': nodeDefault = Number(pair[1]); break; default: getVariables.push(pair[0] + '=' + pair[1]); break; } } }
```

--------------------------------

### Example Taxonomy Output with Ranks

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Example of taxonomy classification output when specific ranks (genus, family, order, superkingdom) are requested using the --lca-ranks parameter. The output includes query accession, taxid, rank name, scientific name, and a semicolon-concatenated string of requested taxa.

```text
NB501858:55:HMHW7BGXB:1:23301:17888:3880        8932    species Columba livia
NB501858:55:HMHW7BGXB:3:12402:9002:13498        131567  no rank cellular organisms
NB501858:55:HMHW7BGXB:4:23405:2354:17246        299123  subspecies      Lonchura striata domestica
NB501858:55:HMHW7BGXB:4:11506:25310:7474        117571  no rank Euteleostomi
NB501858:55:HMHW7BGXB:1:21310:9510:6655 0       no rank unclassified
NB501858:55:HMHW7BGXB:1:11112:6821:9848 1758121 subspecies      Limosa lapponica baueri
NB501858:55:HMHW7BGXB:2:22303:18627:2744        2182385 species Brachybacterium endophyticum
NB501858:55:HMHW7BGXB:4:22410:13879:7449        8825    superorder      Neognathae
NB501858:55:HMHW7BGXB:3:13402:20359:7200        97097   species Phaethon lepturus
```

--------------------------------

### Run Format Benchmark Speed Test

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/fmt/README.md

Execute the speed test for the format-benchmark suite after building.

```bash
make speed-test
```

--------------------------------

### Get Percentage

Source: https://github.com/soedinglab/mmseqs2/blob/master/data/resources/krona_prelude.html

Converts a fraction to a percentage value, rounded to the nearest integer.

```javascript
function getPercentage(fraction) {
return round(fraction * 100);
}
```

--------------------------------

### Enable POWER8 AltiVec Instructions

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Use this flag for PPC64LE systems that support POWER8 AltiVec instructions.

```bash
cmake .. -DHAVE_POWER8=1
```

--------------------------------

### Get ZSTD Version Number

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/doc/zstd_manual.html

Useful for checking the dynamic library version at runtime.

```c
unsigned ZSTD_versionNumber(void);
```

--------------------------------

### Run XXHash Userland Tests

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/contrib/linux-kernel/README.md

Navigate to the test directory, build the Google Test framework, compile the XXHash userland tests, and execute them to verify the xxHash kernel module patch.

```bash
cd test && make googletest && make XXHashUserLandTest && ./XXHashUserLandTest
```

--------------------------------

### Build align

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/libmarv/Readme.md

Compiles the 'align' component of the software. Ensure you have the necessary software requirements installed.

```bash
make align
```

--------------------------------

### Create Zstandard Dictionary

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/README.md

Trains Zstandard on a set of files to create a dictionary for improved small data compression. Specify the training data path and the output dictionary name.

```bash
zstd --train FullPathToTrainingSet/* -o dictionaryName
```

--------------------------------

### Download and Install MMseqs2 Static SSE2 Binary

Source: https://github.com/soedinglab/mmseqs2/blob/master/README.md

Download the slowest static build of MMseqs2 with SSE2 support for very old systems, extract it, and add its bin directory to your PATH.

```bash
wget https://mmseqs.com/latest/mmseqs-linux-sse2.tar.gz; tar xvfz mmseqs-linux-sse2.tar.gz; export PATH=$(pwd)/mmseqs/bin/:$PATH
```

--------------------------------

### Querying the Database (Default Output)

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/libmarv/Readme.md

Queries a constructed database using the 'align' tool. Results are output to stdout in plain text by default. Requires query file and database path.

```bash
./align --query queries.fa(.gz) --db dbfolder/dbname
```

--------------------------------

### Iostreams Formatting Example

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/fmt/README.md

Illustrates the verbosity of iostreams for formatting floating-point numbers compared to printf.

```c++
std::cout << std::setprecision(2) << std::fixed << 1.23456 << "\n";
```

--------------------------------

### Registering a New MMseqs2 Command

Source: https://github.com/soedinglab/mmseqs2/wiki/MMseqs2-Developer-Guide

Example of how a new command is registered in `src/mmseqs.cpp`, including its name, function pointer, argument parsing structure, and documentation.

```cpp
{"search",               search,               &par.searchworkflow,       COMMAND_MAIN,
        "Search with query sequence or profile DB (iteratively) through target sequence DB",
        "Searches with the sequences or profiles query DB through the target sequence DB by running the prefilter tool and the align tool for Smith-Waterman alignment. For each query a results file with sequence matches is written as entry into a database of search results (alignmentDB).\nIn iterative profile search mode, the detected sequences satisfying user-specified criteria are aligned to the query MSA, and the resulting query profile is used for the next search iteration. Iterative profile searches are usually much more sensitive than (and at least as sensitive as) searches with single query sequences.",
        "Martin Steinegger <martin.steinegger@mpibpc.mpg.de>",
        "<i:queryDB> <i:targetDB> <o:alignmentDB> <tmpDir>",
        CITATION_MMSEQS2},
```

--------------------------------

### Find System Zstd Library

Source: https://github.com/soedinglab/mmseqs2/blob/master/CMakeLists.txt

Locates the Zstd library and its include directories if Zstd is installed on the system.

```cmake
include(FindPackageHandleStandardArgs)
find_path(ZSTD_INCLUDE_DIRS NAMES zstd.h REQUIRED)
# We use ZSTD_findDecompressedSize which is only available with ZSTD_STATIC_LINKING_ONLY
find_library(ZSTD_LIBRARIES NAMES libzstd.a libzstd_static REQUIRED)
find_package_handle_standard_args(ZSTD DEFAULT_MSG ZSTD_LIBRARIES ZSTD_INCLUDE_DIRS)
mark_as_advanced(ZSTD_LIBRARIES ZSTD_INCLUDE_DIRS)
include_directories(${ZSTD_INCLUDE_DIRS})
```

--------------------------------

### Create Generic Database

Source: https://github.com/soedinglab/mmseqs2/wiki/Home

Use this command to initialize an empty MMseqs2 database file for generic data, such as header databases.

```bash
awk 'BEGIN { printf("%c%c%c%c",12,0,0,0); exit; }' > seqDb.dbtype
```

--------------------------------

### Write to a File Efficiently

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/fmt/README.md

Example of writing formatted output to a file using fmt::output_file for potentially faster I/O operations compared to fprintf.

```c++
#include <fmt/os.h>

int main() {
  auto out = fmt::output_file("guide.txt");
  out.print("Don't {}", "Panic");
}
```

--------------------------------

### ZSTD_CCtxParam Set/Get Parameter

Source: https://github.com/soedinglab/mmseqs2/blob/master/lib/zstd/doc/zstd_manual.html

Functions for setting and getting individual compression parameters within a `ZSTD_CCtx_params` structure.

```APIDOC
## ZSTD_CCtxParam Set/Get Parameter

### Description
Functions for setting and getting individual compression parameters within a `ZSTD_CCtx_params` structure.

### Functions

- **size_t ZSTD_CCtxParam_setParameter(ZSTD_CCtx_params* params, ZSTD_cParameter param, unsigned value);**
  Sets a single compression parameter, identified by the `ZSTD_cParameter` enum, to the specified `value`. Parameters must be applied to a `ZSTD_CCtx` using `ZSTD_CCtx_setParametersUsingCCtxParams()`. Note: when `value` is an enum, cast it to `unsigned` for proper type checking.
  @result: 0 on success, or an error code (which can be tested with `ZSTD_isError()`).

- **size_t ZSTD_CCtxParam_getParameter(ZSTD_CCtx_params* params, ZSTD_cParameter param, unsigned* value);**
  Gets the current value of a single compression parameter, identified by the `ZSTD_cParameter` enum. The value is stored in the `unsigned* value` pointer.
  @result: 0 on success, or an error code (which can be tested with `ZSTD_isError()`).
```