Softwares & packages forBioinformatics

Here we provide some of the important links of the software and packages which are widely used in the field of bioinformatics


Software Active link
PDB https://www.rcsb.org
NCBI https://www.ncbi.nlm.nih.gov
ExPASy https://www.expasy.org
GeneBank https://www.ncbi.nlm.nih.gov/genbank/
EBI https://www.ebi.ac.uk/
BLAST https://blast.ncbi.nlm.nih.gov/Blast.cgi
BlastClust https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html
CD-HIT http://www.bioinformatics.org/cd-hit/
Psi-Blast https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE=Proteins&PROGRAM=blastp&RUN_PSIBLAST=on
HMMER http://hmmer.org/
ClustalW http://www.clustal.org/
MEGA https://www.megasoftware.net/
David https://david.ncifcrf.gov/tools.jsp
GWBLAST http://crdd.osdd.net/raghava/gwblast/
FTG http://crdd.osdd.net/raghava/ftg/
GWFASTA http://crdd.osdd.net/raghava/ftg/
BioPython https://biopython.org/
ViennaRNA https://www.tbi.univie.ac.at/RNA/
conCavity https://www.tbi.univie.ac.at/RNA/
Boxshade https://embnet.vital-it.ch/software/BOX_form.html
Hhsuite https://aur.archlinux.org/packages/hhsuite/
Cain http://cain.sourceforge.net/
Python-rdkit http://www.rdkit.org/docs/GettingStartedInPython.html
Raccoon http://autodock.scripps.edu/resources/raccoon/
Freediams https://www.bestfreewaredownload.com/freeware/k-search-t-free-freediams-freeware-rpzpehqi.html
Freemedforms https://launchpad.net/ubuntu/+source/freemedforms-project/
openclinica https://openclinica.com/
ABINIT https://www.abinit.org/
Openmax https://www.khronos.org/openmax/
Ccwatcher http://ccwatcher.sourceforge.net/
Kalzium https://www.kde.org/applications/education/kalzium/
Gabedit http://gabedit.sourceforge.net/
Gchem3d http://gchemutils.nongnu.org/gchem3d.html
Gchemcalc http://gchemutils.nongnu.org/gchemcalc.html
GchemPaint http://www.nongnu.org/gchemutils/paint/manual/index.html
Gnome Chemistry Utils http://gchemutils.nongnu.org/
Mopac7r https://www.webmo.net/support/mopac_linux.html
MPQC http://mpqc.org/
Viewmol http://viewmol.sourceforge.net/
XDrawChem http://www.woodsidelabs.com/chemistry/xdrawchem.php
PSI4 http://www.psicode.org/
ABySS 1.3.5 http://www.bcgsc.ca/platform/bioinfo/software/abyss/
mpliconnoise 1.28 https://code.google.com/archive/p/ampliconnoise/
arb 5.5 http://www.arb-home.de/
artemis 13.2 https://www.sanger.ac.uk/science/tools
assembly conversion tools https://genome.leibniz-fli.de/software/roche454ace2caf/
beam2 http://personal.psu.edu/yzz2/software/
bedtools https://code.google.com/archive/p/bedtools/
biosquid https://packages.debian.org/unstable/biosquid
bitseq https://code.google.com/archive/p/bitseq/
bowtie http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
bwa http://bio-bwa.sourceforge.net/
CatchAll http://www.northeastern.edu/catchall/downloads.html
CD-HIT http://www.bioinformatics.org/cd-hit/
chimera.slayer https://www.mothur.org/wiki/Chimera.slayer
CLC Sequence Viewer https://www.qiagenbioinformatics.com/products/clc-sequence-viewer/
ClustalW https://embnet.vital-it.ch/software/ClustalW.html
cortex-con https://launchpad.net/~nebc/+archive/ubuntu/bio-linux/+sourcepub/2753076/+listing-archive-extra
Cufflinks http://cole-trapnell-lab.github.io/cufflinks/
Cytoscape https://cytoscape.org/
Dendroscope3 http://ab.inf.uni-tuebingen.de/software/dendroscope/
Dialign https://bibiserv.cebitec.uni-bielefeld.de/dialign/
Dotter http://sonnhammer.sbc.su.se/Dotter.html
Embassy-domalign https://snapcraft.io/store
EMBOSS https://www.ebi.ac.uk/Tools/emboss/
ESTScan https://sourceforge.net/projects/estscan/files/ESTScan2/
fastDNAml Distribution http://iubio.bio.indiana.edu/soft/molbio/evolve/fastdnaml/fastDNAml.html
FastQC Tutorial https://wiki.hpcc.msu.edu/display/Bioinfo/FastQC+Tutorial/
FastTree http://meta.microbesonline.org/fasttree/
fastx-toolkit https://launchpad.net/ubuntu/+source/fastx-toolkit/0.0.13.1-1/
galaxy-server https://launchpad.net/~nebc/+archive/ubuntu/bio-linux/+build/4055867
Geneious https://www.geneious.com/previous-versions/
GLAM2 http://bioinformatics.org.au/tools/glam2/
GlIMMER http://ccb.jhu.edu/software/glimmer/index.shtml
gnx-tools https://launchpad.net/~tbooth/+archive/ubuntu/ppa1/+sourcepub/2353823/+listing-archive-extra
MyBioSoftware http://www.mybiosoftware.com/handlebar-2-2-2-web-based-sample-inventory-manager.html
JELLYFISH http://www.cbcb.umd.edu/software/jellyfish/
JalView http://www.jalview.org/
jMOTU https://www.softpedia.com/get/Science-CAD/jMOTU.shtml#download
jprofilegrid https://launchpad.net/~nebc/+archive/ubuntu/bio-linux/+sourcepub/2940846/+listing-archive-extra
LASTZ http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
libbiojava-java https://launchpad.net/ubuntu/precise/i386/libbiojava-java/1:1.7.1-1
LUCY https://sourceforge.net/projects/amos/files/Lucy%20-%20mirror/1.19p/
macs https://launchpad.net/ubuntu/+source/macs/2.0.9.1-1/
MAFFT https://mafft.cbrc.jp/alignment/software/

About Raghava

Professor Gajendra P.S. Raghava, Indraprasta Institute of Information Technology, New Delhi is a strong supporter of open source software and open access, all resources developed at his group are free for scientific use.