Nematode phylogenomics #1

Dnr:

SNIC 2017/7-114

Type:

SNAC Small

Principal Investigator:

Oleksandr Holovachov

Affiliation:

Naturhistoriska riksmuseet

Start Date:

2017-08-07

End Date:

2018-09-01

Primary Classification:

10615: Evolutionsbiologi

Webpage:

Allocation

Abstract

Evolutionary studies that use genomic data as a basis for phylogeny involve multiple bioinformatic steps, some of which are computation-heavy. One of the most important steps of analysis involves pairwise comparison of genomic datasets for all species included in the study and produces a list of putatively orthologous genes. These genes undergo further filtering and quality control before they can serve as input data for phylogenomic analysis. The goal of this project is to test two alternative software tools for orthology identification of proteins (HaMStR versus OrthoFinder) to be used for further phylogenomic analysis. The input dataset includes proteomes (protein sequences) for about 100 nematode species. The most comprehensive output from either HaMStR or OrthoFinder will be used for future phylogenomic study that does not require computational resources of SUPR/UPPMAX.