DebianSequenceAnalysis

Short explanation:

This page lists programs which are usefull to the field of sequence analysis. It is mostly software related to sequence alignment, phylogeny, motif finding, and sequence manipulation.

Most column names are self-explanatory. When a licence is listed as "Academic", it means that the program is only free of charge for academic, non-profit research, which makes non-compliant to the DebianFreeSoftwareGuidelines. "Packaging" gives cues about the difficulty of the packaging, or indicates that the program has already been packaged. "Importance" gives cues about what to package first. That is why programs already packaged have nothing written there: it does not mean that they are not important!. "Listed on... " records whether the program is listed on the official DebianMed website.

Integrated environments

Program	Licence	Packaging	Importance	Listed on microbio.wml?
emboss-explorer	GPL	packaged (experimental)		no
Jemboss	GPL	part of pkg-emboss	free	no
wemboss	GPL	perl CGI?	free	no
Pasteur Institute Software Environment (Pise)	GPL	complex	free	no
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?
abiview (pkg-emboss)	GPL	packaged (experimental)		yes
STARS	GPL	depends on Staden	free	no
trev (Staden)	BSD	packaging the whole Staden seems difficlut	vital	yes (Staden)
TraceView	Not found	Depends on JAVA		no

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

Sequence assembly

Program	Licence	Packaging	Importance	Listed on microbio.wml?
CAP3	academic	maybe closed source	not a lot of alternatives	no
ContigViewer	GPL	depends on python	Works on CAP3 output	no
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
SSAHA	GPL	easy ?	popular alternative to BLAT	no
RaveNnA	GPL	big package	free	no
Infernal	GPL	big package	free	no
rsearch	GPL	Depends on squid	free	no
RSmatch	not found	Depends on java and recommends the Vienna package		no
erpin	not found	looks easy		no
BLAT	non-free	no	popular	no
fasta	academic	upstream does not want, but there is one in bio-linux	popular	no
SSAHA2	Academic, maybe closed source	Hopeless: depends on phrap/cross_match	unpackageable	no
wublast	non-free	impossible	unpackageable	no

Pairwise alignment

Program	Licence	Packaging	Importance	Listed on microbio.wml?
NCBI blast	public domain	packaged (main)		yes
CONTRAlign	Public domain	straightforward	free	yes
NeoBio	GPL	depends on java	free, has GUI and command line, and supports multiple algorithms	no
jaligner	GPL	depends on java	has a GUI	no
Yass	GPL	trivial	free	no
foldalign	GPL	should be easy	free	no
sim	not found	trivial	many alternatives... benchmark ?	no
ariadne	disclaimer	build failed on ppc	has a method for determining statistical significance	no
exonerate	LGPL	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
CompLearn NCD	BSD	easy	free and popular	no
laj (viewer)	not found	depends on java		no
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, qscore, a program for scoring multiple alignments, is relevant. (but it has no license). There is also StatSigMa, which is written in C++ and depends on muscle. However, it is beta and has no license.

Multiple alignment viewers and editors

Program	Licence	Packaging	Importance	Listed on microbio.wml?
seaview	GPL	packaged (main)		yes
kalignvu	GPL	easy, may depend on apache	free	no
SOAP	GPL	depends on java	free	no
jalview	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 (main)		yes
Tree display	TreeView X	GPL	packaged (main)		yes
Simulated evolution	Treevolve	not found	unofficial (ens-lyon)	free	no
Simulated evolution	Seq-Gen	BSD	unofficial (ens-lyon)	free	no
Tree export to graphical formats	treeplot	GPL	unofficial (ens-lyon)	free	no
Tree inference	MrBayes	GPL	easy	free and popular	no
Tree inference	QSearch	BSD	easy	free and popular	no
Inference of large trees	RAxML	GPL	simple	free	no
Confidence assessment	CONSEL	GPL	straightforward	free	no
Visualisation of reconciliations	PriMETV	GPL	depends on a 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	Forester	java knowledge needed	looks powerful	no
Tree display	TreeDyn	GPL	depends on Tcl/Tk	looks comprehensive	no
Coloring tree	PhyloView	GPL	perl cgi knowledge needed	free	no
3D Trees	walrus	GPL	java knowledge needed	free, looks powerful	no
Selecting evolution model	ProtTest	GPL	depends on java	free	no
Calculating rates of evolution	r8s	no licence found	make fails		no
Detects families	BranchClust	No licence found	Depends on Perl		no
Merges trees into a graph	Splitstree4		Depends on java		no
Merges trees into a graph	Splitstree		Depends on Tk		no

Motif detection

Program	Licence	Packaging	Importance	Listed on microbio.wml?
PhyloGibbs	GPL	maybe easy	free	no
ELPH	Artistic	looks easy	free	no
CisPlusFinder	LGPL	depends on libtie-ixhash-perl, looks easy	free	no
glam	no licence found	easy	possible alternative to MEME	no
MEME and MAST	academic	unofficial packages	popular	no
MEMERIS	Academic	builds fine	Will not be packaged unless requested	no
MotifEnumerator	not found	one .c file only!		no
AlignACE	Harvard EULA	check with DebianLegal first		no
DME	Academic	Sources not available	maybe too closed	no
SLIMDisc	not found	Depends on Python		no
tacg	GPL	C, easy	powerful	no

Also, the following software is related:

Task	Program	Licence	Packaging	Importance	Listed on microbio.wml?
Motif representation	weblogo/seqlogo	BSD	perl cgi	free	no

Secondary structure of nucleic acids

Task	Program	Licence	Packaging	Importance	Listed on microbio.wml?
display, manipulate and interconnect RNA data	S2S	Public domain	depends on java	free	no
RNA secondary structure	CONTRAfold	BSD	looks easy	free	no
prediction of structural RNAs from sequence aligments	RNAz	Academic	Depends on the Vienna RNA package		no
Predicting structural motifs in aligned nucleotide sequences	ddbRNA	not found	depends on java		no
RNA secondary structure prediction and comparison	Vienna RNA package	Academic	not for beginners		no
RNA secondary structure	RNAshapes	Same as Vienna package (non-free)	Mixture of C and Java		no
Prediction of secondary structure from multiple alignment	RNAlishape	No redistribution fee except media costs	Depends on Haskell		no
Nucleic acid folding	UNAfold	academic	looks easy		no

Micro RNAs

Task	Program	Licence	Packaging	Importance	Listed on microbio.wml?
Target duplex prediction	RNAhybrid	GPL	ITP		no
Hairpin predictor	ScorePin	GPL	compiles with gcj HairpinPredictor.java -I AlgorithmQuick.* --main=HairpinPredictor	free	no
miRNA target discovery	miRanda	GPL	Depends on the Vienna package	would be in "contrib"	no
pre-miRNA predictor	miRNA SVM	GPL	Depends on python, Vienna RNA and GIST	contrib	no
target prediction	MicroTar	BSD	Depends on the Vienna package	contrib	no
Task	Program	Licence	Packaging	Importance	Listed on microbio.wml?

Other software

Task	Program	Licence	Packaging	Importance	Listed on microbio.wml?
Sequence comparisons	Wise2	GPL	packaged (main)		no
Command-line sequence manipulation	EMBOSS	L/GPL	packaged (experimental)		yes
Software suite	delila	unkonwn	depends on pascal		no
Base calling for ABI	autoseq	public domain	looks easy	the only free base caller for linux?	no
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	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	PhyloGrapher	GPL	depends on Tcl/Tk	free	no
Sequence comparisons	Wise2	GPL	packaged main	free	no
Parser for blast output	html4blast	GPL	depends on perl	useful on local installations	no
Parser for blast output	zerg	GPL	C library, perl module	says to be faste	no
Parser for blast output	blast2html	no licence	trivial	Not enough for a package. Group with other scripts?	no
Prediction of coding sequence	Critica	GPL	not tried	free	no
Masking low-complexity strings	xnu	No licence	trivial	used in GCG	no
Masking low-complexity strings	pseg	No licence	trivial	advertised in FASTA	no
Matching EST to genome	est_genome	not found	looks simple	an alternative, sim4, is already packaged	no
Protein analysis	prompt	GPL	depends on R, blast2, java	free	no
Protein analysis	Amino Acid Explorer	Apache	depends on java	free	no
Cis-elements prediction	poxo	Not found	various sub-components		no
Semi-automated sequence analysis	SEALS	Public domain	Depends on webbrowser, hmmer, clustalw, ncbi-toolkit, blast, and other programs	free	no
ORF finding	Virtual Ribosome	GPL	Depends on python	free	no
ORF finding	orfind	Public domain	optionaly depends on webserver	free	no
ORF finfing	geneid	GPL	seems simple to package	free	no
CpG islands prediction	CpGcluster	not found	perl script, could be grouped with others		no
Pretty printing of aligmnents	ESPript	non free (commercial licence is 1000 euros)	fortran program	not packaged unless requested	no
Structural alignment	CE	Academic	should be easy	not packaged unless requested	no
snoRNA discovery	snoSeeker	not found	depends on Vienna and Mfold	would be in "contrib"	no
snoRNA discovery	snoReport	GPL	depends on Vienna	would be in "contrib"	no
snoRNA discovery	snoScan	GPL	depends on biosquid	free	no
snoRNA discovery	snoGPS	GPL	depends on bioperl and biosquid	free	no
tRNA discovery	tRNAscan-SE	GPL	unofficial	free	no
conserved elements discovery	FastCompare	free	looks trivial	free	no
graphical representation	graphDNA	website says opensource	depends on java	free?	no
Categorisation of Hox proteins	HoxPred	CC-GPL	depends on java	free	no
Classification of tRNAs	TFAM	GPL	Depends on BioPerl and coveaf	free	no

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