biotite.application_v2.mmseqs

Interfaces to the MMseqs2 and Foldseek command line programs.

Content

AlignmentDatabase	A database of pairwise alignment results.
AlignmentFormatMode	Output modes accepted by the convertalis command.
AlignmentMode	Values accepted by the alignment_mode option.
ClusterDatabase	A database of sequence clusters.
ClusterMode	Values accepted by the cluster_mode option.
CoverageMode	Values accepted by the cov_mode option.
Database	A database produced by MMseqs2 or Foldseek.
DatabaseType	Sequence types accepted by the MMseqs2 createdb command.
FoldseekApp	A reusable handle to the Foldseek command line program.
MMseqsApp	A reusable handle to the MMseqs2 command line program.
MSADatabase	A database of multiple sequence alignments.
MSAFormatMode	Output modes accepted by the result2msa command.
ProfileDatabase	A database of sequence profiles.
ProfileMatchMode	Column selection modes accepted by the msa2profile command.
SearchType	Values accepted by the search_type option.
SequenceDatabase	An MMseqs2 or Foldseek sequence database.
SequenceIdentityMode	Reference lengths accepted by the seq_id_mode option.
StructureAlignmentType	Values accepted by the alignment_type option of FoldseekApp.
UnpackNameMode	File naming schemes accepted by the unpack_name_mode option.
VerbosityLevel	Values accepted by the v option of every command.
create_database_from_msa	Create an MSA database from one or multiple MSAs.
create_database_from_sequences	Create a database from sequences.
create_database_from_structures	Create a Foldseek database from structures.
get_alignment_table	Export selected alignment columns.
get_alignments	Reconstruct Biotite alignments from an alignment database.
get_clusters	Extract the clusters from a cluster database.
get_matrix_from_profile	Get a position-specific scoring matrix for each profile in a database.
get_msa_from_database	Extract the MSAs from an MSA database.
get_multimer_report	Extract the complex-level hits from a multimer search.
get_sequences_from_database	Extract the sequences from a database.
link_to_ss_database	Link a Foldseek database to its 3Di sub-database.