Page Index - soedinglab/MMseqs2 GitHub Wiki
162 page(s) in this GitHub Wiki:
- Home
- MMseqs2 User Guide
- Table of Contents
- Summary
- System requirements
- Check system requirements under Linux
- Check system requirements under macOS
- Check system requirements under Windows
- Installation
- Install MMseqs2 for Linux
- Install with Homebrew
- Install static Linux version
- Compile from source under Linux
- Compile from source for Linux with GPU support
- Install MMseqs2 for macOS
- Install with Homebrew
- Install static macOS version
- Compile from source under macOS
- Compiling under Clang
- Compiling using GCC
- Install MMseqs2 for Windows (preview)
- Install static Windows version
- Compile from source under Windows
- Use the Docker container
- Building the Docker container
- Set up the Bash/Zsh command completion
- Customizing compilation through CMake
- Getting started
- Usage of MMseqs2 modules
- Easy Workflows in MMseqs2
- Easy-Search
- Easy-Cluster
- Easy-Linclust
- Using MMseqs2 Workflows and Modules
- Downloading databases
- Searching
- convertalis columns
- GPU-accelerated search
- Multi-GPU usage
- Database larger than GPU memory
- Clustering
- Linclust
- Updating a clustered database
- Overview of folders in MMseqs2
- Overview of important MMseqs2 Modules
- Description of workflows
- Batch sequence searching using mmseqs search
- Expanded cluster searches
- Downloading precomputed expandable profile databases
- Searching against expandable profile databases
- Using a precomputed index with expandable profile databases
- Translated sequence searching
- Mapping very similar sequences using mmseqs map
- Clustering databases using mmseqs cluster or mmseqs linclust
- Clustering criteria
- Cascaded clustering
- Clustering modes
- Linear time clustering using mmseqs linclust
- Run Linclust
- Updating a clustering database using mmseqs clusterupdate
- Taxonomy assignment
- Terminology
- Creating a seqTaxDB
- Filtering a seqTaxDB
- The concept of LCA
- Using seqTaxDB for taxonomy assignment
- Taxonomy output and TSV
- Taxonomic ranks
- Taxonomy report in Kraken or Krona style
- Taxonomy top hit report
- Filtering taxonomy output
- Taxonomy annotation of search/cluster results
- Create a seqTaxDB from an existing BLAST database
- Create a seqTaxDB for SILVA
- Create a seqTaxDB for GTDB
- Create a seqTaxDB by manual annotation of a sequence database
- Reciprocal best hit using mmseqs rbh
- Behind the scenes
- Description of core modules
- Computation of prefiltering scores using mmseqs prefilter
- Set sensitivity -s parameter
- Local alignment of prefiltered sequence pairs using mmseqs align
- Clustering sequence database using mmseqs clust
- File formats
- MMseqs2 database format
- Manipulating databases
- Sequence database format
- Prefiltering format
- Alignment format
- Internal alignment format
- Custom alignment format with convertalis
- Clustering format
- Internal cluster format
- Cluster TSV format
- Cluster FASTA-like format
- Extract representative sequence
- Taxonomy format
- Internal taxonomy format
- Taxonomy report in Kraken or Krona style
- LCA TSV
- Profile format
- Parameters that affect profile construction
- Convert a result database into a profile
- Convert an external MSA into a profile
- Extract consensus or sequence information from a profile
- Convert HHsuite HMMs into a profile
- Identifier parsing
- Optimizing sensitivity and consumption of resources
- Prefiltering module
- Memory consumption
- Database splitting runtime slowdown
- Runtime
- Disk space
- Important options for tuning the memory, runtime and disk space usage
- Alignment module
- Memory consumption
- Runtime
- Disk space
- Clustering module
- Memory consumption
- Runtime
- Disk space
- Workflows
- How to run MMseqs2 on multiple servers using MPI
- Write temporary files to local disk when running with MPI
- How to run MMseqs2 on multiple servers using batch systems
- Frequently Asked Questions
- How to set the right alignment coverage to cluster
- Bidirectional coverage
- Target coverage
- Query coverage
- How do parameters of CD-HIT relate to MMseqs2
- How does MMseqs2 compute the sequence identity
- How to restart a search or clustering workflow
- How to control the speed of the search
- How to find the best hit the fastest way
- How does MMseqs2 handle low complexity
- How to redundancy filter sequences with identical length and 100% length overlap
- How to add sequence identities and other alignment information to a clustering result
- How to run external tools for each database entry
- How to compute a multiple alignment for each cluster
- How to manually cascade cluster
- How to cluster using profiles
- How to create a HHblits database
- How to create a target profile database (from PFAM)
- How to cluster a graph given as tsv or m8 file
- How to search small query sets fast
- What is the difference between the map and search workflow
- How to build your own MMseqs2 compatible substitution matrices
- How to create a fake prefiltering for all-vs-all alignments
- How to compute the lowest common ancestor (LCA) of a given set of sequences
- Workflow control parameters
- Search workflow
- Clustering workflow
- Updating workflow
- Environment variables used by MMseqs2
- External libraries used in MMseqs2
- License terms
- MMseqs2 Developer Guide
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- Tutorials
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