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13 votes
Accepted

Computer Virus that infects DNA?

As I understand from your post, the computer virus you are talking about is modifying database (FASTA files) in genetics. That would have a pretty bad impact on research in genetics and medicine. If ...
Remi.b's user avatar
  • 68.1k
7 votes
Accepted

Programs/software to graph biological data

There is no standard software, programming language, or library used for computing and graphing biological data. The R language is commonly used for statistical work, but Python (in conjunction with ...
CircleSquared's user avatar
5 votes
Accepted

What Software could I use to create Diagrams of Biochemical Processes like these?

By posting to this forum, I presume the question is whether the illustrators of this and other biochemistry books used software specifically designed for the purpose of drawing reaction pathways, or, ...
David's user avatar
  • 26k
4 votes

What Software could I use to create Diagrams of Biochemical Processes like these?

In the scientific community, we mostly use a couple tools to draw publication-quality pathway figures: OmniGraffle BioRender These tools are optimized for making the kinds of figures shown in your ...
Alex Reynolds's user avatar
3 votes

What Software could I use to create Diagrams of Biochemical Processes like these?

I have used Draw.IO for similar tasks involving flow charts from scratch. I've also used Adobe Illustrator, usually to modify figures when I have them in a compatible vector graphics format. Finally,...
Bryan Krause's user avatar
  • 46k
3 votes

Is there software or a website where I can browse extinct species?

You can search for species that are "Extinct" or "Extinct in the wild" at the IUCN red list website (International Union for Conservation of Nature and Natural Resources). That list currently includes ...
fileunderwater's user avatar
3 votes

How to generate protein graphics for illustrating articles?

All comments are great, there are numerous software programs that allow you to make such images. Gathering information about the insulin structure By simply clicking on the image in wikipedia it ...
KingBoomie's user avatar
  • 2,380
2 votes

Neuro-simulation tools

Another option, maximal in terms of flexibility albeit also possibly effort, is to write your own. Of course, this presupposes some extra knowledge. However, I think coding your own gives a level of ...
user3658307's user avatar
2 votes

Neuro-simulation tools

I have only used NEURON and the DIY approach for small scale simulations. You can have a look at this comparative table: https://grey.colorado.edu/emergent/index.php/...
vkehayas's user avatar
  • 1,198
2 votes

Significant presence/absence of plant species

I am not quite sure what you mean by "significant presence". If you observe any non-zero number of plants of a given species in a cluster, then the rate at which this plant occur in this cluster is ...
Remi.b's user avatar
  • 68.1k
2 votes

Computer Virus that infects DNA?

This is very silly. All the computer virus is doing is corrupting a text file in a computer database. If someone uses the information in the corrupt file to synthesize actual DNA to modify a living ...
David's user avatar
  • 26k
2 votes

Is there any program or website that allows me to create phylogenetic trees without having to insert an already created dataset?

Have you ever tried using Mesquite? I used it when I taught intro bio lab course as a TA. Basically you try to come up with yes or no questions, and based on how you answer these questions it will ...
user3665690's user avatar
2 votes
Accepted

What software do I need to read-write cas9? and .dna files?

You have a long journey ahead. This guy spent about 4 years to learn what he is doing here. He is using Snapgene software
Retardi Grade's user avatar
2 votes

Is there no good way to run the Vienna RNA tools on Windows?

Against my better nature (I think that this is a question about software, not biology), I offer: https://www.tbi.univie.ac.at/RNA/#download This download works for me to get the precompiled packages. ...
David's user avatar
  • 26k
1 vote
Accepted

What software can be used for simulating human meiosis, taking linkage and recombination into account?

I believe that this is an application of the ms program, which is widely used in population genetics. More recent programs also exist (here is another; here is another, here is another) that may be ...
Maximilian Press's user avatar
1 vote

User friendly phylogenetic tree editing software

Yes, I think that you should consider using MultiSeq which is a package of Visual Molecular Dynamics (VMD). You can use visual molecular dynamics to make phylogenetic trees based on sequence/...
xyz123's user avatar
  • 146
1 vote

Is there a command line molecular cloning tool?

pydna is a python package designed for cloning. Disclaimer: I am the developer. It can be used in a Jupyter notebook to create executable scripts that result in the sequence of a some genetic ...
Björn Johansson's user avatar

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