Introduction | Installation | Load MSA2dist | Sequence Format conversion | Frame aware Biostrings::DNAStringSet translation (cds2aa()) | Pairwise sequence comparison | Calculate pairwise AA distances (aastring2dist()) | Grantham's distance | Calculate pairwise DNA distances (dnastring2dist()) | ape::dist.dna models | IUPAC distance | Coding sequences | Calculating synonymous and nonsynonymous substitutions (dnastring2kaks()) | Using any model from KaKs_Calculator 2.0 | Using indices to calculate Ka/Ks | Codon comparison | Create codon matrix (dnastring2codonmat()) | Calculate average behavior of each codon (codonmat2xy()) | Plot average behavior of each codon | Dxy and FST | Dxy and FST from pre-calculated distance matrix (dist2dxy()) | Dxy and FST directly from Biostrings::DNAStringSet (dnastring2dxy()) | References | Session Info

Vignette - vGWAS basic tutorial | A Brief Tutorial of the R Package vGWAS | Setup Notes | Example | Remarks

CRBHit Basic Vignette | Table of Contents | 1. [Installation] | 2. [Conditional Reciprocal Best Hits - Algorithm] | 2.1. [1. step: sequence similarity search (last)] | 2.1.1. [Input: Coding Sequences (CDS)] | 2.1.2. [Get Longest Isoform from NCBI or ENSEMBL Input (optional)] | 2.1.3. [Sequence Similarity Search] | 2.2. [2. step: filter hits + RBH extraction] | 2.2.1. [Filter blast-like output prior fitting] | 2.2.2. [Custom Filter] | 2.2.3. [Extract RBHs] | 2.3. [3. step: fitting RBHs + get CRBHs] | 2.3.1. [CRBHit pairs - Fitting Parameter] | 3. [Ka/Ks Calculations] | 3.1. [Codon Alignments - cds2codonaln() Function] | 3.2. [MSA2dist::dnastring2kaks() Function] | 3.3. [rbh2kaks() Function] | 4. [References]

Ka/Ks Vignette | Table of Contents | 1. [Conditional reciprocal best hit pairs] | 1.1. [Download Coding sequences (CDS) from NCBI and ENSEMBL] | 1.2. [Get Longest Isoform from NCBI or ENSEMBL Input] | 1.2.1 [isoform2longest()] | 1.2.2 [gtf2longest()] | 1.2.3 [gff2longest()] | 1.3. [Calculate/Filter CRBHit pairs] | 1.4. [Extract Gene/Isoform chromosomal position] | 1.4.1. [Get gene position from NCBI or ENSEMBL Input] | 1.4.2. [Use GTF/GFF3 file to obtain gene position] | 1.5 [Assign Tandem Duplicates] | 1.6 [Synteny with DAGchainer] | 2. [Ka/Ks Calculation] | 3. [Ka/Ks Filtering and Visualisation] | 4. [Homo sapiens vs. Pan troglodytes example] | 5. [References]

Vignette - vGWAS plink tutorial | A Brief Tutorial of the R Package vGWAS using sparse genotype data | Setup Notes | Example | Remarks