SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
anyone who have used the software BioEdit before? bbsinfo General 7 06-01-2015 03:25 AM
introducing BAMseek, a large file viewer for BAM and SAM BAMseek Bioinformatics 11 07-23-2013 08:02 PM
Chip Viewer genseq Ion Torrent 4 04-25-2012 10:37 PM
FASTA Viewer ashkot Bioinformatics 7 02-26-2012 08:23 PM
BAMseek large file viewer - now with VCF and FASTQ support BAMseek Bioinformatics 1 07-25-2011 06:57 PM

Reply
 
Thread Tools
Old 04-11-2012, 12:29 PM   #1
asheenlevrai
Member
 
Location: USA

Join Date: Nov 2011
Posts: 28
Default 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-
asheenlevrai is offline   Reply With Quote
Old 06-08-2012, 07:56 AM   #2
pag
Member
 
Location: CA, USA

Join Date: May 2012
Posts: 72
Default

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,
pag is offline   Reply With Quote
Old 06-08-2012, 09:51 AM   #3
asheenlevrai
Member
 
Location: USA

Join Date: Nov 2011
Posts: 28
Default

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-
asheenlevrai is offline   Reply With Quote
Old 06-08-2012, 11:09 AM   #4
pag
Member
 
Location: CA, USA

Join Date: May 2012
Posts: 72
Default

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).
pag is offline   Reply With Quote
Old 06-08-2012, 01:42 PM   #5
asheenlevrai
Member
 
Location: USA

Join Date: Nov 2011
Posts: 28
Default

Quote:
Originally Posted by pag View Post
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 is offline   Reply With Quote
Old 06-15-2012, 09:19 AM   #6
asheenlevrai
Member
 
Location: USA

Join Date: Nov 2011
Posts: 28
Default

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-
asheenlevrai is offline   Reply With Quote
Reply

Tags
bioedit

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:55 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO