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Software

miRNA

• Software	Program name to be called from command line	Version Lookup
  miRDeep Official Website	auto_blast.pl blastoutparse.pl blastparselect.pl excise_candidate.pl filter_alignments.pl miRDeep.pl overlap.pl permute_structure.pl	echo; echo; git --git-dir=/usr/local/.git --work-tree=/usr/local \ log -p /usr/local/bin/miRDeep.pl |\ head -n 1 | awk '// {print $2}' |\ xargs git --git-dir=/usr/local/.git log -n 1 --name-status
  miRExpress Official Website	Raw_data_parse Trim_adapter alignmentSIMD alignmentSIMDthread analysis statistics_reads	echo; echo; git --git-dir=/usr/local/.git --work-tree=/usr/local \ log -p /usr/local/bin/analysis |\ head -n 1 | awk '// {print $2}' |\ xargs git --git-dir=/usr/local/.git log -n 1 --name-status

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Tools for Short Reads

• Software	Program name to be called from command line	Version Lookup
  bsmap (Bisulfite Sequence MApping Program) Official Website	bsmap	ls -l /usr/local/bin/bsmap* | awk '// {print $8,$9,$10}'
  Soap (Short Oligonucleotide Analysis Package)Official Website	soap soap-denovo soapsnp	ls -l /usr/local/bin/soap* | awk '// {print $8,$9,$10}'
  Eland Official Website	eland_15 eland_15 ... eland_32 ELAND_standalone.pl	which eland_15
  Bowtie Official Website	bowtie	bowtie --version
  Maq Official Website	maq maq_eval.pl maq_plot.pl farm-run.pl	maq maq_eval.pl
  Velvet Official Website	velveth velvetg	velveth | head velvetg | head
  Mosaik Official Website	MosaikAligner MosaikAssembler MosaikBuild MosaikCoverage MosaikJump MosaikMerge MosaikSort MosaikText	MosaikBuild | head -4

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EMBOSS

• Software	Program name to be called from command line	Version Lookup
  EMBOSS Official Website	abiview antigenic backtranambig backtranseq banana biosed btwisted cai chaos charge and many more... View Complete List	embossversion

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Programming

• Software	Program name to be called from command line	Version Lookup
  R Offical Website Programming in R R Manual	R	R --version or ls -l /usr/local/bin/R* | grep -v RNA | awk '// {print $8,$9,$10}'
  Bioperl Offical Website	echo ' #!/usr/bin/perl -w use strict; use Bio::SeqIO; # More perl code goes here ' | perl See FAQ for examples	perl -MBio::Root::Version -e ' print $Bio::Root::Version::VERSION,"\n"'
  C/C++, Python, Ruby, Java, and Perl	gcc python ruby java perl	gcc --version python -V ruby --version javac -version perl --version
  bison	needs to be installed

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Databases

• Software	Program name to be called from command line	Version Lookup
  PostgreSQL Offical Website	psql	psql --version
  PostgreSQL graphical user interface Offical Website	pgadmin3	aptitude show pgadmin3
  MySQL Offical Website	mysql	mysql --version

  
  

Version Control

• Software	Program name to be called from command line	Version Lookup
  Git Offical Website	git	git --version
  Mercurial Offical Website	hg	hg --version
  Subversion (not preferred) Offical Website	svn	svn --version

  
  

Pairwise Alignment

• Software	Program name to be called from command line	Version Lookup
  Blast Official Webiste	blast2 blastall	aptitude show blast2
  HMMER Offical Website	hmmalign hmmbuild hmmcalibrate hmmconvert hmmemit hmmfetch hmmindex hmmpfam hmmsearch	aptitude show hmmer
  SAM Official Webiste	sam2hmmer	sam2hmmer  -v
  Matcher Official Website	matcher	embossversion
  FASTA / SSEARCH / GGSEARCH Official Website	fasta35 ggsearch35 tfastf35 and more (see version lookup)	echo;echo; git --git-dir=/usr/local/.git --work-tree=/usr/local \ log -p /usr/local/bin/list_db |\ head -n 1 | awk '// {print $2}' |\ xargs git --git-dir=/usr/local/.git log -n 1 --name-status
  MUMMER Official Webiste		echo;echo; git --git-dir=/usr/local/.git --work-tree=/usr/local \ log -p /usr/local/bin/mummer |\ head -n 1 | awk '// {print $2}' |\ xargs git --git-dir=/usr/local/.git log -n 1 --name-status
  HMMER3 (beta) Official Link		echo;echo; git --git-dir=/usr/local/.git --work-tree=/usr/local \ log -p /usr/local/bin/hmmsearch* |\ head -n 1 | awk '// {print $2}' |\ xargs git --git-dir=/usr/local/.git log -n 1 --name-status
  UCSC Kent Tools (includes BLAT) Official Website		git --git-dir=/usr/local/.git --work-tree=/usr/local \ log -p /usr/local/bin/blat |\ head -n 1 | awk '// {print $2}' |\ xargs git --git-dir=/usr/local/.git log -n 1 --name-status

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Multiple Sequence Alignment

• Software	Program name to be called from command line	Version Lookup
  T-Coffee Official Website	t_coffee	t_coffee -version
  Clustal Official Website	clustalw clustalwtofasta clustalx clustalw2	clustalw -help clustalw2 -help
  MAFFT Official Website		mafft -asdf 2>&1 | head

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Gene Mapping

• Software	Program name to be called from command line	Version Lookup
  ERANGE Offical Website	altSpliceCounts.py chkSNPrmask.py geneNeighbors.py stallCategory.py and more (see version lookup)	git --git-dir=/usr/local/.git --work-tree=/usr/local \ log -p /usr/local/bin/stallCategory.py |\ head -n 1 | awk '// {print $2}' |\ xargs git --git-dir=/usr/local/.git log -n 1 --name-status
  TopHat Offical Website	tophat	echo; echo; git --git-dir=/usr/local/.git --work-tree=/usr/local \ log -p /usr/local/bin/tophat |\ head -n 1 | awk '// {print $2}' |\ xargs git --git-dir=/usr/local/.git log -n 1 --name-status

  
  

Molecular Dynamics

• Software	Program name to be called from command line	Version Lookup
  NAMD Offical Website	namd-start namd-kill-job namd-kill-all-jobs See: Using-NAMD	/usr/local/src/NAMD_2.6_Source/Linux-amd64-MPI/namd2 -V | head

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Software to be Installed...

Repeat Masking

• RepeatMasker Official Website

  Medium Priority

Pairwise Alignment

• AB-BLAST (was WU-BLAST)

  http://blast.advbiocomp.com/doc/README.html#Licensing Licensing AB-BLAST (freely available to academics)

  
  

Multiple Sequence Alignment

Gene finders

Molecular Evolution

Phylognenetics

Gene family Clustering

Domain searching and functional classification

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