.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH LASTAL "1" "January 2019" "lastal 963" "User Commands"
.SH NAME
lastal \- genome-scale comparison of biological sequences
.SH SYNOPSIS
.B lastal
[\fI\,options\/\fR] \fI\,lastdb-name fasta-sequence-file(s)\/\fR
.SH DESCRIPTION
Find and align similar sequences.
.PP
Cosmetic options:
\fB\-h\fR, \fB\-\-help\fR: show all options and their default settings, and exit
\fB\-V\fR, \fB\-\-version\fR: show version information, and exit
\fB\-v\fR: be verbose: write messages about what lastal is doing
\fB\-f\fR: output format: TAB, MAF, BlastTab, BlastTab+ (default=MAF)
.PP
E\-value options (default settings):
\fB\-D\fR: query letters per random alignment (1e+06)
\fB\-E\fR: maximum expected alignments per square giga (1e+18/D/refSize/numOfStrands)
.PP
Score options (default settings):
\fB\-r\fR: match score   (2 if \fB\-M\fR, else  6 if 0<Q<5, else 1 if DNA)
\fB\-q\fR: mismatch cost (3 if \fB\-M\fR, else 18 if 0<Q<5, else 1 if DNA)
\fB\-p\fR: match/mismatch score matrix (protein\-protein: BL62, DNA\-protein: BL80)
\fB\-a\fR: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21)
\fB\-b\fR: gap extension cost (DNA: 1, protein:  2, 0<Q<5:  9)
\fB\-A\fR: insertion existence cost (a)
\fB\-B\fR: insertion extension cost (b)
\fB\-c\fR: unaligned residue pair cost (off)
\fB\-F\fR: frameshift cost (off)
\fB\-x\fR: maximum score drop for preliminary gapped alignments (z)
\fB\-y\fR: maximum score drop for gapless alignments (min[t*10, x])
\fB\-z\fR: maximum score drop for final gapped alignments (e\-1)
\fB\-d\fR: minimum score for gapless alignments (min[e, t*ln(1000*refSize/n)])
\fB\-e\fR: minimum score for gapped alignments
.PP
Initial\-match options (default settings):
\fB\-m\fR: maximum initial matches per query position (10)
\fB\-l\fR: minimum length for initial matches (1)
\fB\-L\fR: maximum length for initial matches (infinity)
\fB\-k\fR: use initial matches starting at every k\-th position in each query (1)
\fB\-W\fR: use "minimum" positions in sliding windows of W consecutive positions
.PP
Miscellaneous options (default settings):
\fB\-s\fR: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein)
\fB\-S\fR: score matrix applies to forward strand of: 0=reference, 1=query (0)
\fB\-K\fR: omit alignments whose query range lies in >= K others with > score (off)
\fB\-C\fR: omit gapless alignments in >= C others with > score\-per\-length (off)
\fB\-P\fR: number of parallel threads (1)
\fB\-i\fR: query batch size (8 KiB, unless there is > 1 thread or lastdb volume)
\fB\-M\fR: find minimum\-difference alignments (faster but cruder)
\fB\-T\fR: type of alignment: 0=local, 1=overlap (0)
\fB\-n\fR: maximum gapless alignments per query position (infinity if m=0, else m)
\fB\-N\fR: stop after the first N alignments per query strand
\fB\-R\fR: repeat\-marking options (the same as was used for lastdb)
\fB\-u\fR: mask lowercase during extensions: 0=never, 1=gapless,
.IP
2=gapless+postmask, 3=always (2 if lastdb \fB\-c\fR and Q<5, else 0)
.PP
\fB\-w\fR: suppress repeats inside exact matches, offset by <= this distance (1000)
\fB\-G\fR: genetic code file
\fB\-t\fR: 'temperature' for calculating probabilities (1/lambda)
\fB\-g\fR: 'gamma' parameter for gamma\-centroid and LAMA (1)
\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 (3)
.PP
\fB\-Q\fR: input format: 0=fasta or fastq\-ignore, 1=fastq\-sanger, 2=fastq\-solexa,
.IP
3=fastq\-illumina, 4=prb, 5=PSSM (fasta)
.SH "REPORTING BUGS"
Report bugs to: last\-align (ATmark) googlegroups (dot) com
.br
LAST home page: http://last.cbrc.jp/