pkg-descr

"Wise2 is package that is focused on comparing DNA sequences at
the level of its conceptual translation, regardless of sequencing
error and introns. This really is a rewrite of the old wisetools
package, which I wrote about 3 years ago.

It can compare a single protein or a profile HMM to a genomic DNA
sequence, and predict a gene structure. This is algorithm, called
genewise, is one of the algorithms available in Wise2. There are
other algorithms focused on EST data rather than genomic data, as
well as some other algorithm curios."
- from the web site (Ewan Birney)

WWW: http://www.ebi.ac.uk/Wise2/

pkg-message

Welcome to Wise2.2

You must set your WISECONFIGDIR to the config directory before
using the programs:

in (t)csh: setenv WISECONFIGDIR PREFIX/share/wise/
in (ba)sh: export WISECONFIGDIR=PREFIX/share/wise/

To try an example:

cd PREFIX/share/examples/wise
genewise road.pep human.genomic

[Replace 'PREFIX' above with the actual installation prefix,
which by default is '/usr/local'.]

pkg-plist

bin/genomewise
%%PORTDOCS%%%%DOCSDIR%%/README
%%PORTDOCS%%%%DOCSDIR%%/apiend.tex
%%PORTDOCS%%%%DOCSDIR%%/appendix.tex
%%PORTDOCS%%%%DOCSDIR%%/dynamite.tex
%%PORTDOCS%%%%DOCSDIR%%/genewise21.eps
%%PORTDOCS%%%%DOCSDIR%%/genewise6.eps
%%PORTDOCS%%%%DOCSDIR%%/gettex.pl
%%PORTDOCS%%%%DOCSDIR%%/makefile
%%PORTDOCS%%%%DOCSDIR%%/wise2.tex
%%PORTDOCS%%%%DOCSDIR%%/wise2api.tex
%%PORTDOCS%%%%DOCSDIR%%/wise3arch.tex
%%PORTDOCS%%share/examples/wise/README
%%PORTDOCS%%share/examples/wise/db.hmm
%%PORTDOCS%%share/examples/wise/hn_est.fa
%%PORTDOCS%%share/examples/wise/human.genomic
%%PORTDOCS%%share/examples/wise/keratin_intron.human
%%PORTDOCS%%share/examples/wise/keratin_intron.mouse
%%PORTDOCS%%share/examples/wise/pep.fa
%%PORTDOCS%%share/examples/wise/road.pep
%%PORTDOCS%%share/examples/wise/rrm.HMM
%%PORTDOCS%%share/examples/wise/vav.dna
%%PORTDOCS%%share/examples/wise/xeno.cdna
%%PORTDOCS%%share/examples/wise/xeno.pep
share/wise/BLOSUM30.bla
share/wise/BLOSUM45.bla
share/wise/BLOSUM62.bla
share/wise/BLOSUM80.bla
share/wise/aa.rnd
share/wise/blosum30.bla
share/wise/blosum62.bla
share/wise/cb.tmf
share/wise/codon.table
share/wise/gene.stat
share/wise/gon120.bla
share/wise/gon160.bla
share/wise/gon200.bla
share/wise/gon250.bla
share/wise/gon350.bla
share/wise/human.gf
share/wise/human.gp
share/wise/human.stats
share/wise/idenity.bla
share/wise/methods
share/wise/pb.gf
share/wise/pombe.gf
share/wise/tm.pri
share/wise/wise.2
share/wise/wise.per
share/wise/worm.gf
bin/dba
bin/dnal
bin/estwise
bin/estwisedb
bin/genewise
bin/genewisedb
bin/psw
bin/pswdb
%%PORTDOCS%%@dirrm %%DOCSDIR%%
%%PORTDOCS%%@dirrm share/examples/wise
@dirrm share/wise