estwisedb - options: model

-gap

[ 12] gap penalty

-ext

[ 2] extension penalty

-matrix

[blosum62.bla] Comparison matrix

-hname

For single hmms, use this as the name, not filename

-codon

[codon.table] Codon file

-subs

[0.01] Substitution error rate

-indel

[0.01] Insertion/deletion error rate

-null

[syn/flat] Random Model as synchronous or flat [default syn]

-alg

[333/312/312Q] Algorithm used for searching [default 312]

-aalg

[333/333L] Algorithm used for alignment [default 623]

-kbyte

[ 2000] Max number of kilobytes used in alignments calculation

-cut

[20.00] Bits cutoff for reporting in search algorithm

-ecut

[n/a] Evalue cutoff only for searches which can calculate evalues

-aln

[50] Max number of alignments (even if above cut)

-nohis

Don't show histogram on single protein/hmm vs DNA search

-report

[0] Issue a report every x comparisons (default 0 comparisons)