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I have used DNAStar laser gene and VectorNTI in the past for cloning, primer design, sequence alignments, etc but no longer have access to these. Are there any comparable replacement suites or what stand alone packages would you now recommend?

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TO do what? Please explain your actual requirements. –  terdon Feb 17 '14 at 17:15
And for which operating system? –  Chris Feb 17 '14 at 19:10
I should have specified OS. Either OSX or Linux. As for what I want to do with it, I need to be able to at least organize sequences, design primers from large sequences, local alignments, make plasmid maps, search ORFs, develop cloning strategies, etc. I also want to read chromatograms –  ryetochondria Feb 19 '14 at 17:25
All of this you can do with benchling (see answer below). And as it is web based it is not operating system dependent. As far as I know Geneious and GeneDesigner don't work in Linux. –  Gergana Vandova Feb 19 '14 at 18:16
CLC workbench is a decent program as well (see response below). –  Bez May 23 '14 at 13:10

6 Answers 6

I would strongly recommend benchling https://benchling.com

This is an awesome web based tool for cloning, primer design, multiple sequence alignments and everything else you are used to doing with the other tools. It is very user friendly, and most importantly you can share designs with your collaborators. Also, the graphics are very beautiful. I recently started using it and I am really impressed with the technical support they offer: you can chat with them and they would reply within minutes. Also, if there is a feature you would like to have implemented they would definitely consider it. Benchling is free, open source and you might be even able to code up some features yourself.

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Thanks for pointing this out. –  Alan Boyd Feb 19 '14 at 20:15
My pleasure! Are you a benchling user? –  Gergana Vandova Feb 19 '14 at 22:20
Starting from today. –  Alan Boyd Feb 20 '14 at 7:42

I would recommend Galaxy. https://usegalaxy.org/ The system does include primer design, sequence alignments and covers many common bioinformatics tasks.

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I personally use more frequently Geneious for most of the basic every-day manipulations (my university bought a license), but I would recommend Ugene: it's free, open-source, cross-platform and supports batching and scenarios.

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For primer design you can use the Gene Designer: https://www.dna20.com/resources/genedesigner

For sequence alignment you can use BLAST (from the NCBI, also downloadable as a standalone tool)

Of course there are better options that might be more specific for your situation.

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If it's not loo late to contribute, CLC workbench is nice too (http://www.clcbio.com/products/clc-main-workbench/). I only use the free version (http://www.clcbio.com/products/clc-sequence-viewer/) but its very user friendly in terms of the features I have worked with.

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Geneious is probably the strongest standalone package, but real bionformaticians rarely deal with GUI driven programs.

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Why do you say that "real" bioinformaticians rarely use GUIs? Is it just some sort of macho "I'm too cool for that user-friendly stuff" attitude? REAL anythings get the job done with the best tools that are available for their particular problem domain. Sometimes it's text-based utilities, sometimes web-based, sometimes GUI-based. It's not about how much pain you can inflict on yourself, but whether you can get the job done correctly, on time, and on-budget. –  MattDMo Feb 18 '14 at 23:03
@MattDMo It's not just elitism. For sequence manipulation, GUIs are much less efficient. They only make sense for people who have so little competence with programming that the added cost of learning this makes suffering a GUI desirable. –  Superbest Nov 14 '14 at 21:12
@Superbest please back up your statement with data that GUIs are "much less efficient." With today's modern multi-core computers and huge amounts of available RAM, the cost of running a graphical interface is not terribly high, considering that most users will be using one anyway. I am perfectly comfortable using Linux through the command line, and I am rather proficient in Python, but if pointing and clicking makes a one-off job easier than writing a new program for it, I'll do it. You say it's not elitism, but the rest of your comment is as elitist as they come. –  MattDMo Nov 14 '14 at 21:22
They're not inefficient of resource usage, they are inefficient in terms of user time and effort. Many GUI tools are also critically underpowered. The Geneious next-gen alignment functions, for instance, do not output a SAM file (to my knowledge) that you can manipulate with other tools if Geneious functionality is not enough for you. Adding to that is the issue of citing proprietary algorithms in your publications. –  Superbest Nov 14 '14 at 21:30
@MattDMo Also, I'd like you to explain how my comment is "as elitist as they come". –  Superbest Nov 14 '14 at 21:31

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