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Assignments for Computational Biology Fall 2021 at the University of Pittsburgh
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What is an example of another simple function to build a phylogenetic tree? #40

Open mitalibelambe opened 2 years ago

mitalibelambe commented 2 years ago

https://github.com/brouwern/compbio2021/blob/4fc22d26cd66119a177fd9572bd409ffa989216d/KEY-MSA-walkthrough-shroom.Rmd#L839

brouwern commented 2 years ago

we will only use nj() for this test

we may use another function/algo called upgma() which works with distance matrices. its a general form of algo used in both stats and phylogenetics called a clustering alog. another one for distance matrices used on BLAST I believe is called "minimum evolution."

On Mon, Oct 4, 2021 at 12:46 PM mitalibelambe @.***> wrote:

https://github.com/brouwern/compbio2021/blob/4fc22d26cd66119a177fd9572bd409ffa989216d/KEY-MSA-walkthrough-shroom.Rmd#L839

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Lecturer

Department of Biological Sciences https://www.biology.pitt.edu/

University of Pittsburgh

Biostatistics course: brouwern.github.io/BIOSC_1120/index.html

Research Associate

National Aviary, Dept. of Conservation & Field Research https://www.aviary.org/conservation

R code: github.com/brouwern

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