Differences between revisions 60 and 61
Revision 60 as of 2006-05-03 02:50:34
Size: 8219
Comment: Handel: an evolutionary model-based Statistical Alignment package.
Revision 61 as of 2006-05-03 02:57:07
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Comment: ProAlign, a probabilistic multiple alignment program
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||[http://evol-linux1.ulb.ac.be/ueg/ProAlign/ ProAlign]||GPL||depends on java||has a graphical interface||no||

Integrated environments

Program

Licence

Packaging

Importance

Listed on microbio.wml?

[http://emboss.sourceforge.net/Jemboss/ Jemboss]

GPL

part of emboss

free

no

[http://www.pasteur.fr/recherche/unites/sis/Pise/ Pasteur Institute Software Environment (Pise)]

GPL

complex

free

no

many more on http://emboss.sourceforge.net/interfaces/

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

[http://dnptrapper.sourceforge.net/ DNPTrapper]

BSD

depends on Qt and BerkeleyDB

specialised on finishing

no

Database querying by alignment

Program

Licence

Packaging

Importance

Listed on microbio.wml?

NCBI blast

free

packaged (main)

yes

[http://www.sanger.ac.uk/Software/analysis/SSAHA/ SSAHA]

GPL

easy ?

popular alternative to BLAT

no

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

non-free

no

popular

no

[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

[http://www.sanger.ac.uk/Software/analysis/SSAHA2/ SSAHA2]

Academic, maybe closed source

Hopeless: depends on phrap/cross_match

unpackageable

no

[http://blast.wustl.edu/ wublast]

non-free

impossible

unpackageable

no

Multiple alignment

Program

Licence

Packaging

Importance

Listed on microbio.wml?

t-coffee

GPL

packaged ([http://packages.debian.org/t-coffee main])

yes

muscle

Public domain

packaged ([http://packages.debian.org/ main])

yes

clustalw

academic

packaged ([http://packages.debian.org/clustalw non-free])

yes

[http://dialign.gobics.de/ dialign]

LGPL

[http://bugs.debian.org/361682 ITP]

free

yes

[http://dialign-t.gobics.de/ dialign-t]

LGPL

makefile is specific to ia32

better than dialign?

no

[http://msa.cgb.ki.se/cgi-bin/msa.cgi kalign]

GPL

[http://bugs.debian.org/365344 ITP]

free

no

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

public domain

[http://bugs.debian.org/365499 ITP]

the most accurate

no

[http://biowiki.org/HandelPackage Handel]

GPL

part of the [http://sourceforge.net/projects/dart dart] package, which does not build out of the box on powerpc

free

no

[http://evol-linux1.ulb.ac.be/ueg/ProAlign/ ?ProAlign]

GPL

depends on java

has a graphical interface

no

[http://www.bio.inf.uni-jena.de/Software/MARNA/index.html marna]

no licence

depends on t-coffee and on the vienna RNA package

Takes secondary structure of RNAs into account

no

mafft

academic

looks easy

rare

no

prrn

academic

looks easy

rare

no

[http://research.amnh.org/scicomp/projects/malign.php malign]

unclear (discrepancies between files)

impossible for the moment

no

saga

non-redistributable

impossible

obsoleted by t-coffee?

no

[http://theory.med.buffalo.edu/ spem]

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://www.biomedempire.org/ACANA ACANA]

closed source?

not without the source

no

Also, [http://www.drive5.com/qscore/ qscore], a program for scoring multiple alignments, is relevant. (but it has no license).

Multiple alignment viewers

Program

Licence

Packaging

Importance

Listed on microbio.wml?

[http://msa.cgb.ki.se/cgi-bin/msa.cgi kalignvu]

GPL

easy, may depend on apache

free

no

seaview

GPL

contrib

yes

strap

?

depends on java

no

xced

adademic

no sources available

rare

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

Tree display

[http://www.treedyn.org/ ?TreeDyn]

GPL

Strangely, the sources are not available

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

Calculating rates of evolution

[http://ginger.ucdavis.edu/r8s/ r8s]

no licence found

make fails

no

Other software

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Software suite

[http://www.lecb.ncifcrf.gov/~toms/delila/delilaprograms.html delila]

unkonwn

depends on pascal

no

Base calling for ABI

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

public domain

looks easy

the only free base caller for linux?

no

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

QA of mutiple alignments

[http://msa.cgb.ki.se/cgi-bin/msa.cgi mumsa]

GPL

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

Graphical representation of sequence conservation

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

GPL

depends on Tcl/Tk

free

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

Motif searching

[http://zlab.bu.edu/glam/ glam]

no licence found

easy

possible alternative to MEME

no

Motif representation

[http://weblogo.berkeley.edu/ weblogo/seqlogo]

BSD

perl cgi

free

no

Sequence comparisons

[http://www.ebi.ac.uk/Wise2/ Wise2]

GPL

[http://envgen.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/ bio-linux]

free

no

Parser for blast output

[ftp://ftp.pasteur.fr/pub/GenSoft/unix/alignment/Blast_tools/Html4blast/ html4blast]

GPL

depends on perl

useful on local installations

no

Parser for blast output

[http://bioinfo.iq.usp.br/zerg/ zerg]

GPL

C library, perl module

says to be faste

no

Parser for blast output

[http://www.pasteur.fr/~tekaia/HYG/blast2html blast2html]

no licence

trivial

Not enough for a package. Group with other scripts?

no

display, manipulate and interconnect RNA data

[http://bioinformatics.org/S2S/ S2S]

Public domain

depends on java

free

no

prediction of structural RNAs from sequence aligments

[http://www.tbi.univie.ac.at/~wash/RNAz/ RNAz]

Academic

Depends on the Vienna RNA package

no

RNA secondary structure prediction and comparison

[http://www.tbi.univie.ac.at/~ivo/RNA/ Vienna RNA package]

Academic

not for beginners

no


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