Foldseek 6-29e2557

At a glance: Introduced block-aligner for faster alignments, added ungapped prefilter mode, added cluster search support

Major Features

• Introduced block-aligner, a new banded-alignment algorithm that speeds up alignments by ~2x. Check out the block-aligner preprint. Thanks @Daniel-Liu-c0deb0t!
• Added ungapped prefilter mode (--prefilter-mode 1). This is similar to the HHblits prefilter that exhaustively aligns without gaps all queries and targets. This mode has much lower memory requirements and should scale better for single or few query searches. However, it scales worse with many queries.
• Added cluster search support, similar to the search introduced in ColabFold

Features

• Improved README
• Added support for qtmscore and ttmscore in convertalis --format-output
• LDDT computation is now faster

Bug fixes

• --greedy-best-hit search mode is now correctly exposed. Thanks @Pooryamb!
• Removed ANISOU parsing of PDB
• Added missing Foldseek specific convertalis --format-output options to help text

Developers and Maintainers

Foldseek now requires Rust to compile. Please make sure Rust 1.68 or newer is installed, as we have observed issues with 1.64. You can pass -DIGNORE_RUST_VERSION=1 to CMake to ignore the check. Please ensure the Foldseek regression test in ./regression/run_regression.sh passes before shipping Foldseek packages. We also require at least CMake 3.15 now.