.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH LASTAL "1" "February 2024" "lastal 1542" "User Commands"
.SH NAME
lastal \- genome-scale comparison of biological sequences
.SH SYNOPSIS
.B lastal-plain
[\fI\,options\/\fR] \fI\,lastdb-name fasta-sequence-file(s)\/\fR
.SH DESCRIPTION
Find and align similar sequences.
.SS "Cosmetic options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show all options and their default settings, and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
show version information, and exit
.TP
\fB\-v\fR
be verbose: write messages about what lastal is doing
.TP
\fB\-f\fR
output format: TAB, MAF, BlastTab, BlastTab+ (default: MAF)
.SS "E-value options (default settings):"
.TP
\fB\-D\fR
query letters per random alignment (default: 1e+06)
.TP
\fB\-E\fR
max EG2: expected alignments per square giga (1e18/D/refSize/numOfStrands)
.SS "Score options (default settings):"
.TP
\fB\-r\fR
match score   (2 if \fB\-M\fR, else  6 if 1<=Q<=4, else 1 if DNA)
.TP
\fB\-q\fR
mismatch cost (3 if \fB\-M\fR, else 18 if 1<=Q<=4, else 1 if DNA)
.TP
\fB\-p\fR
match/mismatch score matrix (protein\-protein: BL62, DNA\-protein: BL80)
.TP
\fB\-X\fR
N/X is ambiguous in: 0=neither sequence, 1=reference, 2=query, 3=both (0)
.TP
\fB\-a\fR
gap existence cost (DNA: 7, protein: 11, 1<=Q<=4: 21)
.TP
\fB\-b\fR
gap extension cost (DNA: 1, protein:  2, 1<=Q<=4:  9)
.TP
\fB\-A\fR
insertion existence cost (a)
.TP
\fB\-B\fR
insertion extension cost (b)
.TP
\fB\-c\fR
unaligned residue pair cost (off)
.TP
\fB\-F\fR
frameshift cost(s) (off)
.TP
\fB\-x\fR
maximum score drop for preliminary gapped alignments (z)
.TP
\fB\-y\fR
maximum score drop for gapless alignments (min[t*10, x])
.TP
\fB\-z\fR
maximum score drop for final gapped alignments (e\-1)
.TP
\fB\-d\fR
minimum score for gapless alignments (min[e, 2500/n query letters per hit])
.TP
\fB\-e\fR
minimum score for gapped alignments
.SS "Initial-match options (default settings):"
.TP
\fB\-m\fR
maximum initial matches per query position (10)
.TP
\fB\-l\fR
minimum length for initial matches (1)
.TP
\fB\-L\fR
maximum length for initial matches (infinity)
.TP
\fB\-k\fR
use initial matches starting at every k\-th position in each query (1)
.TP
\fB\-W\fR
use "minimum" positions in sliding windows of W consecutive positions
.SS "Miscellaneous options (default settings):"
.TP
\fB\-P\fR
number of parallel threads (default: 1)
.TP
\fB\-K\fR
omit alignments whose query range lies in >= K others with > score (off)
.TP
\fB\-C\fR
omit gapless alignments in >= C others with > score\-per\-length (off)
.TP
\fB\-s\fR
strand: 0=reverse, 1=forward, 2=both (2 if DNA and not lastdb \fB\-S2\fR, else 1)
.TP
\fB\-S\fR
score matrix applies to forward strand of: 0=reference, 1=query (0)
.TP
\fB\-i\fR
query batch size (64M if multi\-volume, else off)
.TP
\fB\-M\fR
find minimum\-difference alignments (faster but cruder)
.TP
\fB\-T\fR
type of alignment: 0=local, 1=overlap (default: 0)
.TP
\fB\-n\fR
maximum gapless alignments per query position (infinity if m=0, else m)
.TP
\fB\-N\fR
stop after the first N alignments per query strand
.TP
\fB\-R\fR
lowercase & simple\-sequence options (the same as was used by lastdb)
.TP
\fB\-U\fR
maximum tandem repeat unit length (100 if \fB\-\-codon\fR else same as lastdb)
.TP
\fB\-u\fR
mask lowercase during extensions: 0=never, 1=gapless,
2=gapless+postmask, 3=always (2 if lastdb \fB\-c\fR and Q!=pssm, else 0)
.TP
\fB\-w\fR
suppress repeats inside exact matches, offset by <= this distance (1000)
.TP
\fB\-G\fR
genetic code (default: 1)
.TP
\fB\-t\fR
\&'temperature' for calculating probabilities (1/lambda)
.TP
\fB\-g\fR
\&'gamma' parameter for gamma\-centroid and LAMA (default: 1)
.TP
\fB\-j\fR
output type: 0=match counts, 1=gapless, 2=redundant gapped, 3=gapped,
.IP
4=column ambiguity estimates, 5=gamma\-centroid, 6=LAMA,
7=expected counts (default: 3)
.TP
\fB\-J\fR
score type: 0=ordinary, 1=full (1 for new\-style frameshifts, else 0)
.TP
\fB\-Q\fR
input format: fastx, keep, sanger, solexa, illumina, prb, pssm
.IP
(default: fasta)
.SS "Split options:"
.TP
\fB\-\-split\fR
do split alignment
.TP
\fB\-\-splice\fR
do spliced alignment
.TP
\fB\-\-split\-f\fR=\fI\,FMT\/\fR
output format: MAF, MAF+
.TP
\fB\-\-split\-d\fR=\fI\,D\/\fR
RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1)
.TP
\fB\-\-split\-c\fR=\fI\,PROB\/\fR
cis\-splice probability per base (default: 0.004)
.TP
\fB\-\-split\-t\fR=\fI\,PROB\/\fR
trans\-splice probability per base (default: 1e\-05)
.TP
\fB\-\-split\-M\fR=\fI\,MEAN\/\fR
mean of ln[intron length] (default: 7.0)
.TP
\fB\-\-split\-S\fR=\fI\,SDEV\/\fR
standard deviation of ln[intron length] (default: 1.7)
.TP
\fB\-\-split\-m\fR=\fI\,PROB\/\fR
maximum mismap probability (default: 1.0)
.TP
\fB\-\-split\-s\fR=\fI\,INT\/\fR
minimum alignment score (default: e OR e+t*ln[100])
.TP
\fB\-\-split\-n\fR
write original, not split, alignments
.TP
\fB\-\-split\-b\fR=\fI\,B\/\fR
maximum memory (default: 8T for split, 8G for spliced)