Build phylogenetic tree with alignment file

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2.9 years ago

Jonathan Yoou ▴ 60

Hi all,

I have a question on tools for building a phylogenetic tree. I have an alignment file of 60 strains from Roary tool (.aln file). And what I want to do is draw a phylogenetic tree based on this (aln file), so I tried FastTree, but it provokes an error saying, "This alignment consists of closely-related and very-long sequences." and it results in a blank nwk file. I also treid EMBL phylogenetic tree webtool, but it also says my file is too big to process.

Does anyone recommend any webtool or local tool I can build the tree??

Thank you in advance.

nwk phylogenetic aln alignment • 1.2k views

ADD COMMENT • link updated 2.9 years ago by Michael 54k • written 2.9 years ago by Jonathan Yoou ▴ 60

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You could try RaXML or iqtree2 on the commandline, but this will take a while too. I suspect that your alignment consists of mostly invariant columns, and those convey no phylogenetic information. You could delete all the positions that are all identical and drastically reduce the size of your input file. This could be done by custom scripts or automatically using gblocks.

ADD REPLY • link 2.9 years ago by Michael 54k

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