Provided by: lambda-align2_2.0.0-2build1_amd64 
NAME
lambda2 searchp - the Local Aligner for Massive Biological DatA
SYNOPSIS
lambda2 searchp [OPTIONS] -q QUERY.fasta -i INDEX.lambda [-o output.m8]
DESCRIPTION
Lambda is a local aligner optimized for many query sequences and searches in protein space. It is
compatible to BLAST, but much faster than BLAST and many other comparable tools.
Detailed information is available in the wiki: <https://github.com/seqan/lambda/wiki>
OPTIONS
-h, --help
Display the help message.
-hh, --full-help
Display the help message with advanced options.
--version
Display version information.
--copyright
Display long copyright information.
-v, --verbosity INTEGER
Display more/less diagnostic output during operation: 0 [only errors]; 1 [default]; 2 [+run-time,
options and statistics]. In range [0..2]. Default: 1.
Input Options:
-q, --query INPUT_FILE
Query sequences. Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*],
.ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the
following extensions: gz, bz2, and bgzf for transparent (de)compression.
-a, --input-alphabet STRING
Alphabet of the query sequences (specify to override auto-detection). Dna sequences will be
translated. One of auto, dna5, and aminoacid. Default: auto.
-g, --genetic-code INTEGER
The translation table to use if input is Dna. See
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c for ids. Default is to use the
same table that was used for the index or 1/CANONICAL if the index was not translated. Default: 0.
-i, --index INPUT_DIRECTORY
The database index (created by the 'lambda mkindexp' command). Valid filetype is: .lambda.
Output Options:
-o, --output OUTPUT_FILE
File to hold reports on hits (.m* are blastall -m* formats; .m8 is tab-seperated, .m9 is tab-
seperated with with comments, .m0 is pairwise format). Valid filetypes are: .sam[.*], .m9[.*],
.m8[.*], .m0[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for
transparent (de)compression. Default: output.m8.
--output-columns STRING
Print specified column combination and/or order (.m8 and .m9 outputs only); call -oc help for more
details. Default: std.
--percent-identity INTEGER
Output only matches above this threshold (checked before e-value check). In range [0..100].
Default: 0.
-e, --e-value DOUBLE
Output only matches that score below this threshold. In range [0..100]. Default: 1e-04.
-n, --num-matches INTEGER
Print at most this number of matches per query. In range [1..10000]. Default: 256.
--sam-with-refheader BOOL
BAM files require all subject names to be written to the header. For SAM this is not required, so
Lambda does not automatically do it to save space (especially for protein database this is a
lot!). If you still want them with SAM, e.g. for better BAM compatibility, use this option. One of
1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: off.
--sam-bam-seq STRING
For BLASTX and TBLASTX the matching protein sequence is "untranslated" and positions retransformed
to the original sequence. For BLASTP and TBLASTN there is no DNA sequence so a "*" is written to
the SEQ column. The matching protein sequence can be written as an optional tag, see --sam-bam-
tags. If set to uniq than the sequence is omitted iff it is identical to the previous match's
subsequence. One of always, uniq, and never. Default: uniq.
--sam-bam-tags STRING
Write the specified optional columns to the SAM/BAM file. Call --sam-bam-tags help for more
details. Default: AS NM ae ai qf.
--sam-bam-clip STRING
Whether to hard-clip or soft-clip the regions beyond the local match. Soft-clipping retains the
full sequence in the output file, but obviously uses more space. One of hard and soft. Default:
hard.
General Options:
-t, --threads INTEGER
number of threads to run concurrently. In range [1..40]. Default: 4.
Seeding / Filtration:
--adaptive-seeding BOOL
Grow the seed if it has too many hits (low complexity filter). One of 1, ON, TRUE, T, YES, 0, OFF,
FALSE, F, and NO. Default: on.
--seed-length INTEGER
Length of the seeds. In range [3..50]. Default: 10.
--seed-offset INTEGER
Offset for seeding (if unset = seed-length/2). In range [1..50]. Default: 5.
--seed-delta INTEGER
maximum seed distance. In range [0..1]. Default: 1.
--seed-delta-increases-length BOOL
Seed delta increases the min. seed length (for affected seeds). One of 1, ON, TRUE, T, YES, 0,
OFF, FALSE, F, and NO. Default: off.
--seed-half-exact BOOL
Allow errors only in second half of seed. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: on.
Miscellaneous Heuristics:
--pre-scoring INTEGER
evaluate score of a region NUM times the size of the seed before extension (0 -> no pre-scoring, 1
-> evaluate seed, n-> area around seed, as well; default = 1 if no reduction is used). In range
[1..10]. Default: 2.
--pre-scoring-threshold DOUBLE
minimum average score per position in pre-scoring region. In range [0..20]. Default: 2.
--filter-putative-duplicates BOOL
filter hits that will likely duplicate a match already found. One of 1, ON, TRUE, T, YES, 0, OFF,
FALSE, F, and NO. Default: on.
--filter-putative-abundant BOOL
If the maximum number of matches per query are found already, stop searching if the remaining
realm looks unfeasible. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
--merge-putative-siblings BOOL
Merge seed from one region, stop searching if the remaining realm looks unfeasable. One of 1, ON,
TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: on.
Scoring:
-s, --scoring-scheme INTEGER
use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80. Default: 62.
--score-gap INTEGER
Score per gap character. In range [-1000..1000]. Default: -1.
--score-gap-open INTEGER
Additional cost for opening gap. In range [-1000..1000]. Default: -11.
Extension:
-x, --x-drop INTEGER
Stop Banded extension if score x below the maximum seen (-1 means no xdrop). In range [-1..1000].
Default: 30.
-b, --band INTEGER
Size of the DP-band used in extension (-3 means log2 of query length; -2 means sqrt of query
length; -1 means full dp; n means band of size 2n+1) In range [-3..1000]. Default: -3.
-m, --extension-mode STRING
Choice of extension algorithms. One of auto, xdrop, and fullSerial. Default: auto.
TUNING
Tuning the seeding parameters and (de)activating alphabet reduction has a strong influence on both speed
and sensitivity. We recommend the following alternative profiles for protein searches:
fast (high similarity): --seed-delta-increases-length on
sensitive (lower similarity): --seed-offset 3
For further information see the wiki: <https://github.com/seqan/lambda/wiki>
LEGAL
lambda2 searchp Copyright: 2013-2019 Hannes Hauswedell, released under the GNU AGPL v3 (or later);
2016-2019 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL
SeqAn Copyright: 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.
In your academic works please cite: Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439
For full copyright and/or warranty information see --copyright.