Internal changes: ----------------- - Default setting of pctopt function has been changed from ignoregappositions = FALSE to ignoregappositions = TRUE. - Citation of published paper of this package has been updated.
Internal changes: ----------------- - pairwiseAlignment() has moved from Biostrings to the pwalign package.
Internal changes: ----------------- - An option to compare viral quasispecies at amino acid level was added to "vqscompare" function ("proteincoding" and "removestopcodon" arguments). - "AAcompare" function added to the package - Documentations updated - Reference in the DESCRIPTION file updated - Github link in README.md fixed
Internal changes: ----------------- - Description file correction · Abbreviation explained - Unnecessary print() in all functions removed
Internal changes: ----------------- - Description file correction · Edit package description (add reference) - "vqsresub" function added
Initial CRAN submission.