| 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/ |