Differences between revisions 46 and 47
Revision 46 as of 2006-10-04 06:24:34
Size: 6436
Comment: Open Source, Extensible Viewer for Microarray Data in the PCL or CDT format
Revision 47 as of 2006-10-19 05:35:29
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Comment: Cluster Database at High Identity with Tolerance
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||Database clustering||[http://bioinformatics.org/cd-hit/ CD-HIT]||Not found, but homepage says open source||Straighytforward|| ||no||

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

RNA mapping

[http://www.gene.com/share/gmap/ GMAP]

no profit, no redistribution of modified versions

impossible?

no

Whole-genome alignments

[http://mummer.sourceforge.net/ mummer]

Artistic

make failed

[http://bugs.debian.org/201761 RFP]

no

Comparative genomics

[http://lagan.stanford.edu/lagan_web/index.shtml Lagan]

GPL

[https://www.bioinformatics.uwaterloo.ca/wiki/index.php?Lagan private repository]

free

no

Comparatige genomics

[http://www.microbialgenomics.org/BSR/ BSR]

[http://www.microbialgenomics.org/BSR/BSR_README.txt non-free]

Prior agreement required

no

Genome Browser

[http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=34513 Generic Genome Browser]

Artistic

maybe not easy

Academic ones are really expensive for commercial use

no

Genome Browser

[http://omicspace.riken.jp/omicBrowse/OmicBrowseRegister.html ?OmicBrowser]

GPL

depends on java

flash plugin required for use

no

Integrated environment

[http://sourceforge.net/projects/gmod/ Generic Model Organism Database (GMOD)]

Artistic

complex

important

no

Genome database

[http://www.acedb.org/ acedb]

(L)GPL

maybe not easy

some programs depend on acedb libs

no

Database schema

[http://fuge.sourceforge.net/ FuGE]

not found

xml schema

no

Generic database framework

[http://www.gusdb.org GUS]

BSD

depends on java and perl

Used by many databases

no

Manipulating gff files

[http://biowiki.org/GffTools gffTools]

no licence

lot of manpages to write!

no

Multiple alignments

[http://baboon.math.berkeley.edu/mavid/ MAVID]

academic

would depend on clustalw and fastdnaml

no

EST clustering

[http://www.ii.uib.no/~ketil/bioinformatics/tools.html xsact]

not found

Haskell program, did not build on ppc

no

Discovery of regulatory regions

[http://www.cs.helsinki.fi/u/kpalin/EEL/ Enhancer Element Locator]

GPL

depends on pytohon

free

no

genomic sequence analysis tools

[http://sourceforge.net/projects/cartwheel Cartwheel Bioinformatics Package]

GPL+LGPL

doesn't seem difficult

no

Genetic maps

[http://carl.agtec.uga.edu/MapMerger/ ?MapMerger]

no licence

php cgi

no

Database of SAGE tags

[http://pbil.univ-lyon1.fr/software/identitag/ identitag]

not found

perl and sh scripts

no

Codon usage analysis

[http://codonw.sourceforge.net/ CodonW]

GPL

maybe easy

free

no

Visualisation of annotations

[http://genome.jouy.inra.fr/MuGeN/ MuGeN]

Not found

Depends on gtk, xml, dbi, bioperl, ...

no

Gene predicion

[http://analysis.ccgb.umn.edu/diogenes/ Diogenes]

Not found

./configure && make fails, but it seems easy to fix

no

Rearrangements analysis

[http://www.cs.unm.edu/~moret/GRAPPA/ Grappa]

GPL

straightforward

free

no

Clustering analysis (+GUI)

[http://woldlab.caltech.edu/compClust/ compClust]

[http://woldlab.caltech.edu/compClust/LICENSE.txt MLX]

[http://woldlab.caltech.edu/compClust/debian_install.shtml unofficial package]

Did not check if the license is DFSG-free...

no

Database clustering

[http://bioinformatics.org/cd-hit/ CD-HIT]

Not found, but homepage says open source

Straighytforward

no

cis-regulatory element analysis

[http://cistematic.caltech.edu/ cistematic]

MIT

depends on python and sqlite

free

no

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Microarrays

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Suite

[http://www.tm4.org/ TM4]

artistic

depends on java

free

no

Microarrays

[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/11/1540 SNOMAD]

GPL

depends on R

free

no

Microarrays

[http://genopolis.btbs.unimib.it/genopolis/material/mattia/private_mattia.htm amda]

GPL

R package depending on bioconductor

free

no

Image analysis for microarrays

[http://www.cs.wustl.edu/~jbuhler/dapple/ Dapple]

GPL

depends on Qt, FFTW

free

no

Microarrays

[http://db.systemsbiology.net/software/VERAandSAM/ Vera, Sam]

not found

looks easy

no

Normalisation

[http://www.transcriptome.ens.fr/goulphar/ Goulphar]

GPL

R module depending on Bioconductor

free

no

Genome-scale oligonucleotide design

[http://berry.engin.umich.edu/oligoarray2_1/ ?OligoArray 2.1]

GPL

Depends on Java

free

no

False Discovery Rate

[http://www.stjuderesearch.org/depts/biostats/fdrlibrary/index.html FDRlibrary]

not found

R library

no

False Discovery Rate

[http://www-stat.stanford.edu/~tibs/SAM/Rdist/index.html samr]

LGPL

R library

free

no

Visualisation

[http://jtreeview.sourceforge.net/ Java ?TreeView]

GPL

[http://bioinformatics.pzr.uni-rostock.de/~moeller/debian/treeview/ unofficial]

free or contrib ?

yes

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Repeats

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Repeat masking

[http://www.ii.uib.no/~ketil/bioinformatics/tools.html RBR]

Not found

[http://www.ii.uib.no/~ketil/bioinformatics/tools.html unfficial]

no

Repeats analysis

[https://nbcr.sdsc.edu/euler/ ?RepeatGluer]

Not found

straightforward

no

Repeat finding

[http://repeatscout.bioprojects.org/ ?RepeatScout]

Not found

straightforward

no

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Genome assembling

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

BAC scaffolding

[http://www.bcgsc.ca/bioinfo/software/FASSI FASSI]

GPL

trivial

free

no

BAC scaffolding

[http://www.agcol.arizona.edu/software/fpc/ fpc]

Academic

no

Base calling

[http://www.broad.mit.edu/ftp/distribution/software/Bass/ bass]

BSD with advertising clause

Does not compile out of the box

no

Base calling

[http://www.in-machina.com/~reece/autoseq/ autoseq]

Public domain

Old C++ which may not be compatible with recent gcc

free

no

Band calling

[http://www.sanger.ac.uk/Software/Image/ Image]

unknown

did not find the sources

no

Assembling

[http://sourceforge.net/projects/wgs-assembler/ Whole Genome Assembler]

GPL

free

no

Clustering

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Clustering of SAGE expression

[http://www.bcgsc.ca/bioinfo/ge/treebuilder/ TreeBuilder3D]

GPL

depends on java

no


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