nail 0.4.0

Release Assets

OS	Architecture	Link
MacOS	Universal	Download
MacOS	Intel 64 bit	Download
MacOS	ARM 64 bit (Apple Silicon)	Download
Linux	Intel/AMD 64 bit	Download
Linux	ARM 64 bit	Download
Windows	Intel/AMD 64 bit	Download

On MacOS, you'll see the following message when you try to run nail:

"nail" cannot be opened because the developer cannot be verified.

To fix this, you can run the following command:

sudo xattr -dr com.apple.quarantine <path to binary>

0.3.0

BREAKING

• the seed subcommand has been removed from the CLI (use nail search --only-seed instead)
• many CLI flag names have been changed

Features

• the CLI has been refactored, with several new options:
  • -s prints out pipeline summary statistics
  • -x prints alignments to stdout, doesn't write tabular output (useful for small scale experimentation)
  • --double-seed seeds alignments at two MRE targets (this was done by default in the last release) (note: this is not yet implemented for sequence to sequence search)
  • --only-seed does what nail seed used to do
  • --seeds-out <PATH> saves seeds produced during a normal run of nail search to <PATH>
  • --no-null2 turns off the null two (composition bias) score adjustment
• FASTA input files are now streamed from disk, enabling search of much larger target databases

Bug fixes

• fixed some subtle bugs relating to score calculations
• fixed some bugs relating to determining alignment boundaries
• fixed some bugs in the target/query positions shown in alignment output
• fixed some issues causing overallocation of memory

0.2.0

BREAKING

• the prep and align subcommands have been removed from the CLI
• no longer support MSA (.sto) query files

Features

• no longer depends on hmmbuild
• added support for sequence to sequence search
• gained a bit of sensitivity by running mmseqs search at two profile relative entropy targets
• the null two (composition bias) score correction has been improved for sparse alignment
• tabular results formatting improved

0.1.0

This is the initial 0.1.0 release. The library is unfinished, unstable, and largely undocumented.