malt-run(1) on Linux
The text 4ab7994fe43f, as Debian 13 (Trixie), Debian 12 (Bookworm) shipped it. The page shows this text now.
Sequences aligner using MALT (MEGAN alignment tool)
Flags it lists
-
--alignmentType -
--alignments -
--band -
--conFile -
--format -
--forwardOnly -
--gapExtend -
--gapOpen -
--gzipAligned -
--gzipAlignments -
--gzipUnaligned -
--help -
--inFile -
--includeUnaligned -
--index -
--lcaCoveragePercent -
--magnitudes -
--matchScore -
--maxAlignmentsPerQuery -
--maxAlignmentsPerRef -
--maxExpected -
--maxSeedsPerFrame -
--maxSeedsPerRef -
--maxTables -
--memoryMode -
--minBitScore -
--minPercentIdentity -
--minPercentIdentityLCA -
--minSupport -
--minSupportPercent -
--mismatchScore -
--mode -
--numThreads -
--outAligned -
--outUnaligned -
--output -
--replicateQueryCache -
--replicateQueryCacheBits -
--reverseOnly -
--samSoftClip -
--seedShift -
--setK -
--setLambda -
--sparseSAM -
--subMatrix -
--topPercent -
--useMinPercentIdentityFilterLCA -
--verbose -
--weightedLCA -
--xPart -
-K -
-a -
-at -
-b -
-bd -
-cf -
-d -
-e -
-f -
-fo -
-ge -
-go -
-h -
-i -
-id -
-iu -
-la -
-lcp -
-m -
-ma -
-mag -
-mem -
-mif -
-mm -
-mpi -
-mq -
-mrf -
-mt -
-o -
-oa -
-ou -
-psm -
-ro -
-rqc -
-rqcb -
-sh -
-spf -
-spr -
-sps -
-ssc -
-sup -
-supp -
-t -
-top -
-v -
-wlca -
-xP -
-za -
-zal -
-zul