seqToPhy: Produces the phylogenetic tree graph from sequence file

In helen307/phyMSAViewer: Provide Phylogenetic tree and MSA visualization from Uniprot IDs

Description

A function that produces a phylogenetic tree based on the fasta file uploaded by the users.

Usage

seqToPhy(mySeqs)

Arguments

mySeqs

A AAStringSet of sequences, length of each sequence varies.

Value

Returns a graph of a phylogenetic tree calculated on the sequence dataset along with its full MSA plot.

References

1. Code for retrieving Uniprot data were borrowed from: http://rforbiochemists.blogspot.com/2016/12/drawing-simple-phylogenetic-tree-of.html

2. Pages, H., Aboyoun, P., Gentleman, R., & DebRoy, S. (2016). Biostrings: String objects representing biological sequences, and matching algorithms. R package version, 2(0), 10-18129.

3. Paradis, E., Claude, J., & Strimmer, K. (2004). APE: analyses of phylogenetics and evolution in R language. Bioinformatics, 20(2), 289-290.

4. Yu, G., Smith, D. K., Zhu, H., Guan, Y., & Lam, T. T. Y. (2017). ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution, 8(1), 28-36.

Examples

## Not run: 
# Use the mySeqs dataset for this function:
seqToPhy(mySeqs)
# Access the phylogenetic tree with MSA plot directly.

## End(Not run)

helen307/phyMSAViewer documentation built on Jan. 1, 2021, 3:16 a.m.