MSA2dist - MSA2dist calculates pairwise distances for DNAStringSet/AAStringSet using custom scoring, conducts codon analyses (including dNdS), and estimates Dxy/FST
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calculations which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances. DNAStringSet alignments can be analysed as codon alignments to look for synonymous and nonsynonymous substitutions (dN/dS) in a parallelised fashion using a variety of substitution models. Non-aligned coding sequences can be directly used to construct pairwise codon alignments (global/local) and calculate dN/dS without any external dependencies. In addition, MSA2dist provides population genetic analyses, including the calculation of nucleotide divergence between populations (Dxy) and genetic differentiation statistics (FST) from aligned sequence data.
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alignmentsequencinggeneticsgobioconductor-packagebioinformaticsdndsdnds-estimationiupackaksmsa2distmultiple-sequence-alignmentscore-matrixcpp
6.61 score 4 stars 3 dependents 19 scripts
CRBHits - Conditional reciprocal best hits (CRBHits) in R
CRBHits calculates conditional reciprocal best hit (CRBHit) pairs and subsequently can classify tandem duplicates, assign syntney groups and calculate Ka/Ks values.
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softwarealignmentgeneticsbioinformaticsdndsdnds-estimationjosskakslastpairwise-comparisonreciprocal-blast-hitssynteny
3.68 score 4 stars 12 scriptsvGWAS - Variance Heterogeneity Genome-wide Association Study - Reimplementation
The package reimplementation provides models and tests for variance heterogeneity genome-wide association study (vGWAS).
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gwasvgwas
3.30 score 2 stars 6 scripts