LASTAL(1)

📦
version 1654 · 7 versions
, in ubuntu stonking

🌸 NAME 🌸

lastal — genome-scale comparison of biological sequences 💖 (the page you're reading is LASTAL(1), filed under User Commands, bestie, in case you were wondering 🫶)

✨ SYNOPSIS ✨

lastal-plain [options] lastdb-name fasta-sequence-file(s)

🦋 DESCRIPTION 🦋

Find and align similar sequences. That's it, that's the whole assignment — you hand it a lastdb-name and some fasta-sequence-file(s), and it goes and finds the similar ones and lines them up. Iconic behaviour, no notes. 👑

🎀 Cosmetic options:

The little settings that decide how lastal presents and talks. Slay.

  • -h, --help — shows you literally every single option plus the default settings each one ships with, then peaces out. 👋
  • -V, --version — prints version info and exits. Short and sweet.
  • -v — be verbose: it writes messages about what lastal is doing while it's doing it. Yapper mode, lovingly.
  • -2 — paired query sequences. 🫶
  • -f — output format, aka pick your aesthetic: TAB, MAF, BlastTab, BlastTab+ (default: MAF)

💜 E-value options (default settings):

  • -D — query letters per random alignment (default: 1e+06)
  • -H — expected total number of random alignments for all the sequences
  • -E — max EG2: expected number of random alignments per square giga

🔥 Score options (default settings):

This is where you tune the scoring, and there are a lot of knobs. We're tuning them all, fr fr.

  • -r — match score (2 if -M, else 1)
  • -q — mismatch cost (3 if -M, else 1)
  • -p — match/mismatch score matrix (DNA-DNA: HUMSUM, protein-protein: BLOSUM62, DNA-protein: BLOSUM80)
  • -X — where N/X is ambiguous: 0=neither sequence, 1=reference, 2=query, 3=both (0)
  • -a — gap existence cost (24 if HUMSUM, else 11 if protein reference, else 7)
  • -b — gap extension cost (1 if HUMSUM, else 2 if protein reference, else 1)
  • -A — insertion existence cost (a)
  • -B — insertion extension cost (b)
  • -c — unaligned residue pair cost (off)
  • -F — frameshift cost(s) (off)
  • -x — maximum score drop for preliminary gapped alignments (z)
  • -y — maximum score drop for gapless alignments (min[t*10, x])
  • -z — maximum score drop for final gapped alignments (e-1)
  • -d — minimum score for gapless alignments (min[e, 2500/n query letters per hit])
  • -e — minimum score for gapped alignments

🌈 Initial-match options (default settings):

Where the search starts and how it decides which spots are even worth a look. Main character decisions only.

  • -m — maximum initial matches per query position (10)
  • -l — minimum length for initial matches (1)
  • -L — maximum length for initial matches (infinity)
  • -k — use initial matches starting at every k-th position in each query (1)
  • -W — use "minimum" positions in sliding windows of W consecutive positions

🧚 Miscellaneous options (default settings):

The grab-bag. Everything cute and chaotic lives here. 💅

  • -P — number of parallel threads (default: 1)
  • -K — omit alignments whose query range lies in >= K others with > score (off)
  • -C — omit gapless alignments in >= C others with > score-per-length (off)
  • -s — strand: 0=reverse, 1=forward, 2=both (2 if DNA and not lastdb -S2, else 1)
  • --reverse — reverse the query sequences 🙃
  • -S — use score matrix: 0=as-is, 1=on query forward strands (0)
  • -i — query batch size (64M if multi-volume, else off)
  • -M — find minimum-difference alignments (faster but cruder)
  • -T — type of alignment: 0=local, 1=overlap (default: 0)
  • -n — maximum gapless alignments per query position (infinity if m=0, else m)
  • -N — stop after the first N alignments per query strand
  • -R — lowercase & simple-sequence options (the same as was used by lastdb)
  • -U — maximum tandem repeat unit length (100 if --codon else same as lastdb)
  • -u — mask lowercase during extensions: 0=never, 1=gapless, 2=gapless+postmask, 3=always (2 if lastdb -c and Q!=pssm, else 0)
  • -w — suppress repeats inside exact matches, offset by <= this distance (1000)
  • -G — genetic code (default: 1)
  • -t — 'temperature' for calculating probabilities (1/lambda)
  • -g — 'gamma' parameter for gamma-centroid and LAMA (default: 1)
  • -j — output type: 0=match counts, 1=gapless, 2=redundant gapped, 3=gapped, 4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA, 7=expected counts (default: 3)
  • -J — score type: 0=ordinary, 1=full (1 for new-style frameshifts, else 0)
  • -Q — input format: fastx, keep, sanger, solexa, illumina, prb, pssm (default: fasta)

🌸 Split options:

For when a sequence is not one neat little unit and you gotta deal with the split / spliced situation. 🦋

  • --split — do split alignment
  • --splice — do spliced alignment
  • --split-f=FMT — output format: MAF, MAF+
  • --split-d=D — RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1)
  • --split-c=PROB — cis-splice probability per base (default: 0.004)
  • --split-t=PROB — trans-splice probability per base (default: 1e-05)
  • --split-M=MEAN — mean of ln[intron length] (default: 7.0)
  • --split-S=SDEV — standard deviation of ln[intron length] (default: 1.7)
  • --split-m=PROB — maximum mismap probability (default: 1.0)
  • --split-s=INT — minimum alignment score (default: e OR e+t*ln[100])
  • --split-n — write original, not split, alignments
  • --split-b=B — maximum memory (default: 8T for split, 8G for spliced)
💖 And that's the whole page, bestie. Every flag, every default, every =PROB and =MEAN, all of it, untouched. Go align something gorgeous. ✨

Version lastal 1654, dated August 2026 — ty for reading, mwah, stan a genome-scale aligner today 🎀👑💅

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