Question: Any alternative (free, open source tool) for Geneious software for phylogenetic analysis?
1
gravatar for Jurat Shahidin
23 months ago by
Chicago, IL, USA
Jurat Shahidin80 wrote:

Dear all:

I have downloaded Geneious software trial version https://www.geneious.com/, but now it is expired. As a fresh level grad student, I can't afford to pay full version of Geneious software. I aware that Geneious has abundant features to analyze NGS data. My expectation is to find tools that relatively similar to Geneious. My major intent is to carry out phylogenetic analysis.Can anyone recommend the better alternative for Geneious tools? Is there any free, open source software tools that can be alternative for Geneious? My colleague is not well comfortable with R environment, so we are seeking tools that require less programming input. Can anyone give possible aid or point out which library we can use?

ADD COMMENTlink modified 23 months ago by vmicrobio240 • written 23 months ago by Jurat Shahidin80
1

the universe is full of free softwares: bwa, bowtie, igv ....

' want a GUI ?

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ADD REPLYlink modified 23 months ago • written 23 months ago by Pierre Lindenbaum122k

Hi:

Yeah, any GUI or hand-on tools, or R package could. More specifically, I am looking for possible R packages, or hand-on software tools (free, open source, MAC user) that can be applied on phylogenetic analysis? I am looking for the tool that easy to work with and which also comfortable for researcher without a programming background. Could you list out possible tools or packages I can look at? Thanks

ADD REPLYlink modified 23 months ago • written 23 months ago by Jurat Shahidin80
1

I'd say you need to be a bit more specific with what you mean by "phylogenetic analyses". If this is just "I want to draw a tree", there are plenty of GUI tools for this. E.g make alignments with Clustal, draw a tree with Dendroscope/FigTree etc.

You'll pretty quickly hit bottlenecks if you're limiting yourself to GUI tools though.

ADD REPLYlink written 23 months ago by Joe14k
3
gravatar for genomax
23 months ago by
genomax71k
United States
genomax71k wrote:

MEGA should fit the bill.

ADD COMMENTlink written 23 months ago by genomax71k

@genomax:

MEGA looks good. Thanks for your help :)

ADD REPLYlink written 23 months ago by Jurat Shahidin80
3
gravatar for george.ry
23 months ago by
george.ry1.1k
United Kingdom
george.ry1.1k wrote:

You can also have a look at UGENE as an alternative to Geneious.

ADD COMMENTlink modified 23 months ago • written 23 months ago by george.ry1.1k

Thank you very much. I'll give it shot

ADD REPLYlink modified 23 months ago • written 23 months ago by Jurat Shahidin80
2
gravatar for vmicrobio
23 months ago by
vmicrobio240
vmicrobio240 wrote:

Have a look at Jalview

ADD COMMENTlink modified 23 months ago • written 23 months ago by vmicrobio240

Thanks for your help :)

ADD REPLYlink written 23 months ago by Jurat Shahidin80
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