Good day, I understand you have done some work already, but you may want to try my PhyloMill pipeline. It will do exactly what you need. It is written in Python, not R. You will need to give it the names of ingroup and outgroup taxa and which loci you want to use. If the loci you want to use are not predefined in PhyloMill, I can create the definitions, just let me know which loci you want to use.
PhyloMill will actually do a lot more than just download and align sequences, it will filter mislabeled sequences, reverse-complement if needed, etc. It will also create a consensus sequence when multiple GI accessions are available for that taxon and locus. https://github.com/karolisr/krpy Peace, Karolis Ramanauskas Department of Biological Sciences University of Illinois at Chicago 840 W. Taylor St. SEL 4093 M/C 067 Chicago, IL 60607 E-Mail: kram...@uic.edu > From: "cheny...@hotmail.com" <cheny...@hotmail.com> > Subject: [R-sig-phylo] use R to download the DNA barcode sequence of a list of species from GenBank > Date: July 13, 2014 10:39:13 AM CDT > To: r-sig-phylo <r-sig-phylo@r-project.org> > > Dear All, > > I have a list of about 2,000 plant species, and want to construct a phylogenetic tree for them. I'd like to use the DNA barcode data availabe in GenBank. Then I will first need to download these DNA sequences from the Internet. I know that read.GenBank in package "ape" is capable to do it if I have the GenBank accession numbers. But what I only have now is their species names. Does anybody know which R function can batch-process it with only species names from GenBank? > > Many thanks in advance. > Yuxin > > > > Yuxin Chen > Phd Candidate > School of Life Sciences > Sun Yat-sen University > Guangzhou, P. R. China, 510006 > cheny...@gmail.com or cheny...@mail2.sysu.edu.cn > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
