analyzePairwise: Analyze pairwise alignment this is helper function for...
In oacar/synal: Synteny Alignment and Analysis for Saccharomyces sensu stricto

Analyze pairwise alignment this is helper function for analyze script. Creates a df for every overlapping orf

1 2	analyzePairwise(typeName, outputDirectory, orfName, startAA, startDNA, stopAA, subalign, aa, df, identifier = "best")

`typeName`	species name
`outputDirectory`	folder path for reading input files
`orfName`	identifier for ORF. SGD name if annotated
`startAA`	aminoacid start codons calculated by `startCodon`
`startDNA`	dna start codons calculated by `startCodon`
`stopAA`	aa stop codons calculated by `stopCodon`
`subalign`	dna level subalignment
`aa`	aminoacid translation using subalignment
`df`	df for reference orf values
`identifier`	identifier for the overlapping orf name. it will be used for file names as well.