UCSC genome species color names

[Pamela Paré]

Esteemed, 

 

I used the multiple alignment of the ucsc genome browser to compose a figure. 

 

As shown in the attached figure, some species are named in blue and others in green. 

 

Please, I would like to know the reason for this difference as I was questioned by an article reviewer. 

 

Thankful, 

Pamela Paré

PhD. Genetics & Molecular Biology

Livre de vírus. www.avast.com.

[Matthew Speir]

Hello, Pamela. 

Thank you for your question about multiple alignments in the UCSC Genome Browser. 

The colors are there to allow one to distinguish between different clades. For example, in this Genome Browser session, in the 100-way alignment the species "Rhesus" is blue and "Mouse" is green. If you go to the configuration page for the 100-way, you can see that "Rhesus" is in the "Primate" clade and "Mouse" is in the "Euarchontoglires" clade. This alternating pattern holds for the rest of the clades on the configuration page as well, meaning that those in "Laurasiatheria" will be blue, those in "Afrotheria" green, "Mammal" blue, and so on. 

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues? Host a workshop: http://bit.ly/ucscTraining

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Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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