Chromatogram viewers

Program

Licence

Packaging

Importance

Listed on microbio.wml?

[http://neelix.molbiol.ox.ac.uk:8080/userweb/mchan/stars/ STARS]

GPL

depends on Staden

free

no

trev (Staden)

BSD

packaging the whole Staden seems difficlut

vital

yes (Staden)

abiview (Emboss)

GPL

Debian-Bioinformatics

vital

yes (emboss)

Abiview has a better command line interface, and trev has a better gui.

Sequence assembly

Program

Licence

Packaging

Importance

Listed on microbio.wml?

[http://seq.cs.iastate.edu/ CAP3]

academic

maybe closed source

not a lot of alternatives

no

[http://www.atgc.org/Py_ContigViewer/ ?ContigViewer]

GPL

depends on python

Works on CAP3 output

no

Multiple alignment

Program

Licence

Packaging

Importance

Listed on microbio.wml?

t-coffee

GPL

main

free

yes

clustalw

academic

non-free

very popular

yes

muscle

Public domain

main

free

no

mafft

academic

looks easy

rare

no

prrn

academic

looks easy

rare

no

dialign

proprietary ?

no

rare ?

no

[http://bio.math.berkeley.edu/amap/ amap]

public domain

looks easy. Not to be confused with the [http://packages.debian.org/unstable/net/amap amap] network tool...

specialised in protein alignments

no

[http://probcons.stanford.edu/ probcons]

public domain

looks easy

specialised in protein alignments

no

Phylogenetic analysis

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Tree display and manipulation

njplot

Artistic

main

free

yes

Tree display

?TreeView X

GPL

[http://bugs.debian.org/352506 ITP]

SVG output

yes

Tree display

Phylodendron

pre-release of 1996

java knowledge needed

nice output

no

Tree display and manipulation

ATV

[http://www.genetics.wustl.edu/eddy/forester/forester_distribution/LICENSE.txt Forester]

java knowledge needed

looks powerful

no

Coloring tree

[http://www.biomedcentral.com/1471-2105/7/79/abstract ?PhyloView]

GPL

perl cgi knowledge needed

free

no

3D Trees

[http://www.caida.org/tools/visualization/walrus/ walrus]

GPL

java knowledge needed

free, looks powerful

no

Tree inference

?MrBayes

GPL

free

no

Other software

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Command-line sequence manipulation

EMBOSS

L/GPL

unofficial

vital

yes

Multiple alignment (graphic)

pipmaker

GPL

looks easy

free alternative to vista?

no

Multiple alignment (graphic)

vista

academic

downloading sources require registration

popular

no

Multiple alignment (graphic)

mussa

GPL

looks easy

free

no

Pairwise alignment

[http://www.ebi.ac.uk/~guy/exonerate exonerate]

LGPL

[http://www.ebi.ac.uk/~guy/exonerate/debian/ in progress]

free

no

Comparative sequence analysis

FamilyJewelsII

LGPL or GPL, have to look in the cvs

depends on FLTK

free

no

Alignment editor

xced

adademic

no sources available

rare

no

Graphical representation of sequence conservation

[http://atgc.org/PhyloGrapher/PhyloGrapher_Welcome.html ?PhyloGrapher]

GPL

depends on Tcl/Tk

free

no

Database querying by sequence alignment

[http://www.genomeblat.com/genomeblat/blatfaq.asp BLAT]

non-free

no

popular

no

Database querying by sequence alignment

[http://fasta.bioch.virginia.edu/fasta/ fasta]

[ftp://ftp.virginia.edu/pub/fasta/COPYRIGHT academic]

[http://lists.debian.org/debian-med/2005/05/msg00028.html upstream does not want], but there is one in [http://envgen.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ bio-linux]

popular

no

Motif searching

[http://meme.sdsc.edu/meme/intro.html MEME and MAST]

academic

[https://www.bioinformatics.uwaterloo.ca/wiki/index.php?refs=Local%20Debian%20Repository private repository]

popular

no


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