Manually editing alignments on a mac


#1

Hi All,

I’m wondering what software folks use for automatically aligning sequences and then manually editing those alignments on macs?

I know there’s lots of software out there, but I’m wondering if there’s something I’ve missed. In principle I like the offerings in Geneious (it includes various plug-ins for automated alignment, and a very serviceable manual editor), but the pricetag is a bit steep if that’s all you want it for…

Cheers,

Rob


#2

Seaview is free (http://doua.prabi.fr/software/seaview).

You can align with Muscle or ClustalW directly in it, and you can manually edit the alignment and select regions you want to keep for phylogenetic reconstruction (or run Gblocks). Finally, you can run tree reconstructions (using Phyml, distance methods or parsimony) directly in it too.

Cheers,

Laura


#3

Aliview is a newer option that has been extremely useful: http://www.ormbunkar.se/aliview/

Some of the alignment editing actions (e.g. clicking and dragging chunks) aren’t obvious, but easy to use once you figure them out.

Martin


#4

I use Mesquite for my manual aligning. Its the successor to MacClade and hands down the best for manual adjustments.


#5

You’ve probably already come across this, but Se-Al (link) is fantastic if you haven’t upgraded to Lion or beyond. I’ve started working on a web implementation of Se-Al in HTML5 and JS (github), which would provide a free cross-platform manual editor, but it has limited functionality right now.


#6

Hi Art,

Just come across this post. I was just think about whether to do a SeAl like editor in JavaScript. I will take a look at what you have done and see if I can help in anyway.


#7

This is absolutely great. Se-Al was my editor of choice until the mac os got away. Geneious provides similar functionality, but at a pretty huge price if you’re only interested in manual alignment.


#8

Please try to do so. I loved Se-Al.


#9

I know of some people that keep an old installation of OS X just to use Se-Al…

I’ve heard of a way (ref http://blog.steventroughtonsmith.com/post/109040361205/mpw-carbon-and-building-classic-mac-os-apps-in-os) to compile old Carbon programs so they run on modern systems, but I couldn’t find the source for Se-Al to test it.


#10

Base-By-Base is a java tool from Virology.ca


#11

Can Base-By-Base or any other java-based tool handle very large alignments? My experience with JalView and some other java apps convinced me that screen redrawing an/or other issues got VERY slow when huge alignments were in play, whereas AliView (Mac) and BioEdit (Windows) could handle huge alignments very nicely. So, is Base-By-Base a superior tool, of just an option that is acceptable when needed for small jobs?


#12

Not sure if this is too late but Mathieu Fourment and Eddie Holmes rewrote Se-Al as Seqotron: https://github.com/4ment/seqotron

I was just starting off in phylogenetics when Se-Al use was waning, so I’m not sure how faithful of a re-implementation Seqotron is, but it’s definitely smoother than Geneious.


#13

Ah, fond memories of Se-Al.

Define “huge alignments”…? BBB is made for long sequences (poxvirus genomes = 200-300kb, perhaps a dozen or two), it’s not made for 1000s of sequences, even if they’re small. Just tried to load 1000 1kb sequences, it loaded after about 30sec and it allowed me to scroll around and edit the alignment. Not sure if the alignment tools would crash if I tried to align them. Just aligned with Muscle… quick to align, very slow to import aligned data back to BBB. So better to align first.

BBB has a variety of unique features, so it depends on what you want to do with the alignment. We use it for GenBank files of poxvirus genomes, so it knows about annotation of genes.


#14

Bioedit: https://guangchuangyu.github.io/2016/03/yet-an-unofficial-bioedit-for-osx/