Integrated environments

Program

Licence

Packaging

Importance

Listed on microbio.wml?

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

GPL

part of ["pkg-emboss"]

free

no

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

GPL

complex

free

no

[http://www.bioinformatics.org/SMS/index.html SMS]

GPL

javascript and html

free

no

many more on http://emboss.sourceforge.net/interfaces/, due to be prepared for Debian in the ["pkg-emboss"] effort.

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 (["pkg-emboss"])

GPL

Debian-Bioinformatics

vital

yes (["pkg-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

Program

Licence

Packaging

Importance

Listed on microbio.wml?

NCBI blast

free

packaged (main)

yes

HMMER

GPL

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

Pairwise alignment

Program

Licence

Packaging

Importance

Listed on microbio.wml?

NCBI blast

public domain

packaged ([http://packages.debian.org/unstable/science/blast2 main])

yes

[http://contra.stanford.edu/contralign/ CONTRAlign]

Public domain

straightforward

still in beta, wait for release

yes

[http://neobio.sourceforge.net/ ?NeoBio]

GPL

depends on java

free, has GUI and command line, and supports multiple algorithms

no

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

GPL

depends on java

has a GUI

no

[http://bioinfo.lifl.fr/yass/ Yass]

GPL

trivial

free

no

[http://foldalign.kvl.dk/software/index.html foldalign]

GPL

should be easy

free

no

[ftp://br.expasy.org/pub/lalnview/sim204.c sim]

not found

trivial

many alternatives... benchmark ?

no

[http://www.well.ox.ac.uk/ariadne/ ariadne]

[http://www.well.ox.ac.uk/ariadne/disclaimer.shtml disclaimer]

build failed on ppc

has a method for determining statistical significance

no

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

LGPL

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

free

no

lalign

academic

part of the fasta package

unredistributable (see above)

no

prss

academic

part of the fasta package

unredistributable (see above)

no

[http://globin.cse.psu.edu/java/laj/ laj] (viewer)

not found

depends on java

no

[http://pbil.univ-lyon1.fr/software/lalnview.html lalnview] (viewer)

GPL

depends on fltk and pdflib

free (contrib)

no

Multiple alignment

The multiple alignment programs have been transferred to a separate page, SequenceAlignment.

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

Multiple alignment viewers and editors

Program

Licence

Packaging

Importance

Listed on microbio.wml?

seaview

GPL

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

yes

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

GPL

easy, may depend on apache

free

no

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

GPL

depends on java

free

no

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

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

yes

Tree display

?TreeView X

GPL

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

yes

Simulated evolution

[http://evolve.zoo.ox.ac.uk/software.html?name=Treevolve Treevolve]

not found

unofficial ([http://dept-info.labri.fr/~danjean/deb.html#treevolve ens-lyon])

free

no

Simulated evolution

[http://evolve.zoo.ox.ac.uk/software.html?name=Seq-Gen Seq-Gen]

BSD

unofficial ([http://dept-info.labri.fr/~danjean/deb.html#seqgen ens-lyon])

free

no

Tree export to graphical formats

[http://www.cnrs-gif.fr/pge/bioinfo/treeplot/ treeplot]

GPL

unofficial ([http://dept-info.labri.fr/~danjean/deb.html#treeplot ens-lyon])

free

no

Confidence assessment

[http://www.is.titech.ac.jp/~shimo/prog/consel/ CONSEL]

GPL

straightforward

free

no

Visualisation of reconciliations

[http://prime.sbc.su.se/primetv/ PriMETV]

GPL

depends on a [http://prime.sbc.su.se/primetv/plotutils.html patched version] of the GNU plotutils

free

no

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

depends on Tcl/Tk

looks comprehensive

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

Selecting evolution model

[http://darwin.uvigo.es/software/prottest.html ?ProtTest]

GPL

depends on java

free

no

Calculating rates of evolution

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

no licence found

make fails

no

Motif detection

Program

Licence

Packaging

Importance

Listed on microbio.wml?

[http://www.biozentrum.unibas.ch/~nimwegen/cgi-bin/phylogibbs.cgi ?PhyloGibbs]

GPL

maybe easy

free

no

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

no licence found

easy

possible alternative to MEME

no

[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

[http://faculty.cs.tamu.edu/shsze/motifenumerator/ ?MotifEnumerator]

not found

one .c file only!

no

[http://atlas.med.harvard.edu/ AlignACE]

[http://atlas.med.harvard.edu/download/index.html Harvard EULA]

check with DebianLegal first

no

[http://rulai.cshl.edu/dme/index.shtml DME]

Academic

Sources not available

maybe too closed

no

Also, the following software is related:

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Motif representation

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

BSD

perl cgi

free

no

Other software

Task

Program

Licence

Packaging

Importance

Listed on microbio.wml?

Sequence comparisons

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

GPL

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

free

no

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

["pkg-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

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

Sequence comparisons

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

GPL

packaged [http://packages.debian.org/unstable/science/wise main]

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

Predicting structural motifs in aligned nucleotide sequences

[http://www.tigem.it/Research/Personal%20Web%20Page_files/dibernardo/Website/frame_software.htm ddbRNA]

not found

depends on java

no

RNA secondary structure prediction and comparison

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

Academic

not for beginners

no

Prediction of coding sequence

[http://geta.life.uiuc.edu/~gary/programs/CRITICA.html Critica]

GPL

not tried

free

no

Masking low-complexity strings

[http://blast.wustl.edu/pub/xnu/ xnu]

No licence

trivial

used in GCG

no

Masking low-complexity strings

[http://blast.wustl.edu/pub/nseg/pseg/ pseg]

No licence

trivial

advertised in FASTA

no

Matching EST to genome

[http://www.well.ox.ac.uk/~rmott/ESTGENOME/est_genome.shtml est_genome]

not found

looks simple

an alternative, sim4, is already packaged

no

Protein analysis

[http://webclu.bio.wzw.tum.de/prompt/ prompt]

GPL

depends on R, blast2, java

free

no

Protein analysis

[http://www.evolvingcode.net:8080/aaindex/tools/ Amino Acid Explorer]

Apache

depends on java

free

no

Cis-elements prediction

[http://www.bioinfo.biocenter.helsinki.fi/poxo poxo]

Not found

various sub-components

no

Semi-automated sequence analysis

[http://www.ncbi.nlm.nih.gov/CBBresearch/Walker/SEALS/ SEALS]

Public domain

Depends on webbrowser, hmmer, clustalw, ncbi-toolkit, blast, and other programs

free

no


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