I would like to create a phylogenetic tree by inputting a family (ex: Boidae) and collecting all information on children species available from the ncbi database, and with that information plot a tree.
If this is not possible, is it possible to take occurence record names (from GBIF, for example) put them into a matrix of speces, genera, families, and then turn that into a tree?
These are the packages I've attempted to use to accomplish this so far to no avail:
library("taxize")
library("brranching")
library("phylocomr")
library("ape")
library("phytools")
library("paleobioDB")
library("geiger")
library("timetree")
library("rentrez")
library("Biostrings")
library("ggtree")
The workflow would be:
1) acquire occurence data from GBIF
2) sequester family, genus, and species names
3) search the family, genus and species names in the ncbi database to collect all pertinent phylogenetic records
4) condense information into a tree file
5) plot a tree
I think I figured something out, but its not very pretty.
########################################
library("metacoder")
library("rotl")
library("vegan")
library("dplyr")
library("taxize")
library("ape")
library("Biostrings")
library("ggplot2")
library("ggtree")
library("taxize")
library("rentrez")
########################################
#Use the name_suggest function to download records for many species based on higher taxonomic ranks switch "family name" to your choice fmily
fam
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