promoterwise - options

-s

query start position restriction

-t

query end position restriction

-u

target start position restriction

-v

target end position restriction

-lhwindow

sequence window given to alignment, default 50

-lhseed

seed score cutoff in bits, defualt 10.0

-lhaln

aln score cutoff, default 8.0 bits

-lhscore

sort final list by score (default by position)

-lhreject

[none/query/both] - overlap rejection criteria in greedy assembly [query]

-lhmax

maximum number of processed hits - default 20000

-hitoutput

[pseudoblast/xml/tab] pseudoblast by default

-hithelp

more detailed help on hitlist formats

-dymem

memory style [default/linear/explicit]

-kbyte

memory amount to use [4000]

-

$$no$$

dycache

implicitly cache dy matrix usage (default yes)

-dydebug

drop into dynamite dp matrix debugger

-paldebug

print PackAln after debugger run if used

-help

show help options

-version

show version and compile info

-silent

No messages on stderr

-quiet

No report on stderr

-erroroffstd

No warning messages to stderr

-errorlog

[file] Log warning messages to file