Types of analyses supported at Sheffield

Population genetics & genomics

• GENEPOP, FSTAT, ARLEQUIN – genetic differentiation & diversity analyses.
• STRUCTURE, STRUCTURE HARVESTER, CLUMPP, DISTRUCT – estimating and visualising genetic clusters.
• SPAGEDI, TESS – spatial patterns of genetic diversity.
• MIGRATE – quantify past gene flow.
• MSVAR – calculating the size and timing of changes in population size.

Example images:

STRUCTURE

TESS

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For large data sets, such as high numbers of SNPs, genome re-sequencing or ddRAD projects:

• PLINK, POPGENOME – population genetics summary stats and basic analyses.
• STACKS, POPOOLATION – genotyping SNPs from ddRAD experiments.
• SAMTOOLS, VCFTOOLS – editing & filtering SNP files.
• BAYESCAN – detecting outlier loci.
• GENABEL – for genome-wide association studies.
• fastSTRUCTURE, DISTRUCT, NGSadmix, PCA using adegenet, fineRADstructure, RADpainter – estimating and visualising genetic clusters.

Example images:

GENABEL

PCA

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Relatedness, parentage & pedigree analyses

• ML-RELATE, RELATED – to estimate pairwise relatedness values.
• CERVUS, COLONY – parentage/sibship analysis, paternity assignment.
• MASTERBAYES – pedigree reconstruction, parentage analysis.

Example image:

COLONY

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Metabarcoding to identify species (eg for diet analysis, eDNA & parasite detection)

We support metabarcoding for a range of applications such as diet analysis, biodiversity assessment from environmental DNA, parasite detection and MHC typing.

The follow software convert Illumina MiSeq raw sequence data to taxonomic/genotype output:

• TRIMMOMATIC, FASTQC, FLASH – assess quality, trim and align sequences.
• USEARCH, MOTHUR, QIIME, BLAST, MEGAN – cluster and categorise sequences.
• ACACIA, AmpliSAT, jMHC – genotype MHC loci.

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Phylogenetics

• BEAST, MRBAYES – inferring phylogenies.

Example image:

BEAST