BioEdit file viewer for mac

asheenlevrai · 04-11-2012, 01:29 PM

Hi everyone,

Does anyone knows how to view (and print) BioEdit alignment files on a mac?
I would be very happy if anything exists with the option to display same bases as a dot (it makes it much easier to spot mismatches).

These are fasta files (.fsa), I can open them in text mode but this is really not convenient for alignments :s

I tried eBioX, but the display/print options are very limited (cannot edit sequence title length or style; cannot print in landscape orientation; etc)

Thanks a lot for your help
-a-

pag · 06-08-2012, 08:56 AM

on Mac you could use Geneious to display the fasta. You may have to rename the file as .fasta (for nucleotide fastas at least)

another thing that could work for you is Consed, but it's a complicated procedure to install that.

other packages are macvector, vectorNTI (if that still exists), and seaview,

asheenlevrai · 06-08-2012, 10:51 AM

Thank you

I didn't try Geneious nor Vector NTI since they are not free... (oh and because I hate Vector NTI...)
I didn't try Consed because of the reasons you mentioned

As far as I remember, Macvector can't do what I want (I didn't double check)

However, although the graphics are terrible (I felt like I was back in the 80's), Seaview seem to do everything I need and even more...

Thanks a lot for the hint

Best
-a-

pag · 06-08-2012, 12:09 PM

The last time I used Geneious, which I admit was about 4 years ago now, it was free to academic users in stripped-down form. The stripped down form could do almost anything you could ever want, and would periodically (about one weekday per 2-4 weeks) would give you access to the full features.

I don't like some of the stretching and compressions it does with chromatograms, but it was overall a pretty solid mac/linux option.

I agree that VectorNTI is huge, unwieldy and is fairly useless. I'm glad seaview does what you'd like.

The last time I was using a mac regularly I would use a combination of Geneious and BioEdit (via a Windows virtual environment).

asheenlevrai · 06-08-2012, 02:42 PM

Quote:

Originally Posted by pag

The last time I was using a mac regularly I would use a combination of Geneious and BioEdit (via a Windows virtual environment).

Well, yeah, we run BioEdit under WINE on mac but there are limitations... We can't print or access our NAS for instance... We can't open sequence files directly neither: we have to launch BioEdit and then select file->open...

Tx again,
-a-

asheenlevrai · 06-15-2012, 10:19 AM

Apparently in Seaview you can't create a sequence over 5kb... (it crops the sequence if you try to paste more than 5kb)
If you open a file (created with bioedit) containing sequences over 5kb, Seaview can handle that just fine...
weird...
-a-

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04-11-2012, 01:29 PM	#1
asheenlevrai Member Location: USA Join Date: Nov 2011 Posts: 28	BioEdit file viewer for mac Hi everyone, Does anyone knows how to view (and print) BioEdit alignment files on a mac? I would be very happy if anything exists with the option to display same bases as a dot (it makes it much easier to spot mismatches). These are fasta files (.fsa), I can open them in text mode but this is really not convenient for alignments :s I tried eBioX, but the display/print options are very limited (cannot edit sequence title length or style; cannot print in landscape orientation; etc) Thanks a lot for your help -a-

06-08-2012, 08:56 AM	#2
pag Member Location: CA, USA Join Date: May 2012 Posts: 72	on Mac you could use Geneious to display the fasta. You may have to rename the file as .fasta (for nucleotide fastas at least) another thing that could work for you is Consed, but it's a complicated procedure to install that. other packages are macvector, vectorNTI (if that still exists), and seaview,

06-08-2012, 10:51 AM	#3
asheenlevrai Member Location: USA Join Date: Nov 2011 Posts: 28	Thank you I didn't try Geneious nor Vector NTI since they are not free... (oh and because I hate Vector NTI...) I didn't try Consed because of the reasons you mentioned As far as I remember, Macvector can't do what I want (I didn't double check) However, although the graphics are terrible (I felt like I was back in the 80's), Seaview seem to do everything I need and even more... Thanks a lot for the hint Best -a-

06-08-2012, 12:09 PM	#4
pag Member Location: CA, USA Join Date: May 2012 Posts: 72	The last time I used Geneious, which I admit was about 4 years ago now, it was free to academic users in stripped-down form. The stripped down form could do almost anything you could ever want, and would periodically (about one weekday per 2-4 weeks) would give you access to the full features. I don't like some of the stretching and compressions it does with chromatograms, but it was overall a pretty solid mac/linux option. I agree that VectorNTI is huge, unwieldy and is fairly useless. I'm glad seaview does what you'd like. The last time I was using a mac regularly I would use a combination of Geneious and BioEdit (via a Windows virtual environment).

06-15-2012, 10:19 AM	#6
asheenlevrai Member Location: USA Join Date: Nov 2011 Posts: 28	Apparently in Seaview you can't create a sequence over 5kb... (it crops the sequence if you try to paste more than 5kb) If you open a file (created with bioedit) containing sequences over 5kb, Seaview can handle that just fine... weird... -a-