Question

Any alternative (free, open source tool) for Geneious software for phylogenetic analysis?

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6.5 years ago

Jurat Shahidin ▴ 100

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?

ngs sequencing Geneious phylogenetic analysis • 17k views

ADD COMMENT • link updated 6.5 years ago by vmicrobio ▴ 290 • written 6.5 years ago by Jurat Shahidin ▴ 100

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

' want a GUI ?

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ADD REPLY • link 6.5 years ago by Pierre Lindenbaum 161k

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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 REPLY • link 6.5 years ago by Jurat Shahidin ▴ 100

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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 REPLY • link 6.5 years ago by Joe 21k

score 3 · Accepted Answer · 2017-10-09

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6.5 years ago

GenoMax 141k

MEGA should fit the bill.

ADD COMMENT • link 6.5 years ago by GenoMax 141k

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@genomax:

MEGA looks good. Thanks for your help :)

ADD REPLY • link 6.5 years ago by Jurat Shahidin ▴ 100

score 3 · Accepted Answer · 2017-10-09

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6.5 years ago

george.ry ★ 1.2k

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

ADD COMMENT • link 6.5 years ago by george.ry ★ 1.2k

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Thank you very much. I'll give it shot

ADD REPLY • link 6.5 years ago by Jurat Shahidin ▴ 100

score 2 · Accepted Answer · 2017-10-09

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6.5 years ago

vmicrobio ▴ 290

Have a look at Jalview

ADD COMMENT • link 6.5 years ago by vmicrobio ▴ 290

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Thanks for your help :)

ADD REPLY • link 6.5 years ago by Jurat Shahidin ▴ 100