LASTAL5(1)

🦋 LASTAL5(1) 🦋

okay so bestie, this is the manual page for lastal5, living in the User Commands section, and it's literally about genome-scale comparison of biological sequences. yes the whole genome. no cap. let's get into it 💅

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🌸 NAME 🌸

lastal5 — genome-scale comparison of biological sequences 🧬✨

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🌈 SYNOPSIS 🌈

lastal5-plain [options] lastdb-name fasta-sequence-file(s)

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💖 DESCRIPTION 💖

Find and align similar sequences. that's the whole vibe, but the details are where it ATE. 🫶

🎀 Cosmetic options:

• -h, --help — show all options and their default settings, and exit. your little cheat sheet, bestie 💅
• -V, --version — show version information, and exit. identity check moment ✨
• -v — be verbose: write messages about what lastal is doing. she's narrating her own life, iconic 👑
• -f — output format: TAB, MAF, BlastTab, BlastTab+ (default: MAF)

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🔥 E-value options (default settings):

• -D — query letters per random alignment (1e+06)
• -E — maximum expected alignments per square giga (1e+18/D/refSize/numOfStrands)

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💜 Score options (default settings):

• -r — match score (2 if -M, else 6 if 1<=Q<=4, else 1 if DNA)
• -q — mismatch cost (3 if -M, else 18 if 1<=Q<=4, else 1 if DNA)
• -p — match/mismatch score matrix (protein-protein: BL62, DNA-protein: BL80)
• -X — N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both (0)
• -a — gap existence cost (DNA: 7, protein: 11, 1<=Q<=4: 21)
• -b — gap extension cost (DNA: 1, protein: 2, 1<=Q<=4: 9)
• -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

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✨ Initial-match options (default settings):

• -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

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🌟 Miscellaneous options (default settings):

• -s — strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein)
• -S — score matrix applies to forward strand of: 0=reference, 1=query (0)
• -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)
• -P — number of parallel threads (1)
• -i — query batch size (64M if multi-volume, else off)
• -M — find minimum-difference alignments (faster but cruder). lowkey she's speedrunning 🏃‍♀️💨
• -T — type of alignment: 0=local, 1=overlap (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 — 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 (1)
• -t — 'temperature' for calculating probabilities (1/lambda)
• -g — 'gamma' parameter for gamma-centroid and LAMA (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 (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)

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🧚 Split options:

• --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)

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and that's the whole page, bestie 🫶 this was lastal5 version 1447, dated February 2023, and honestly? she ate and left no crumbs. go align something iconic 💖✨🦋