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publishable phylogenetic trees

prylogenetic trees phylogeny software

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#1 El Crazy Xabi

El Crazy Xabi

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Posted 03 July 2013 - 06:02 PM

Hi guys,

I have to do some phylogenies for new species description and I'm looking for some software which allows to do some cool things with the trees, especially being able to set the scientific name in italics but not the strain or accession number.

I've seen plenty of trees like the one attached in related publications, but I couldn't find what software is used to do something so good-looking. Any ideas?

Thank you!!

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#2 El Crazy Xabi

El Crazy Xabi

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Excellent

Posted 24 July 2013 - 10:18 PM

In case anyone is interested on this, I found some solutions to make trees like that.

For colours, there are few options in TreeDyn and FigTree (both free).

To use different fonts in names and accession numbers, you need to create an annotation file. Both programs prviously mentioned can accept annotation files but they might be different formats
For TreeDyn I make the alignments and everything prior the final tree using accession numbers and an annotation file with this structure

ID_in_tree Variable_1 {value_a} Variable_2 {value_b}
Using the binomial names as variable 1 and the GenBank accession number (or other sequence or strain ID) as variable 2, just import annotations and select to substitute the ID in tree by the name with the font you choose (italics) and add the accession ID with another font





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