Changes in version 1.11.1 (2024-11-14)                 

BUG FIXES

  - fixed pal2nal
  - fixed aastring2aabin to return alignment

NEW FEATURES

  - added globalDeletionAA

                 Changes in version 1.7.5 (2024-03-28)                  

BUG FIXES

  - fixed dnastring2kaks to work with local alignments
  - fixed indices2kaks to work with local alignments
  - fixed cds2codonaln to work with local alignments
  - fixed cdsstring2codonaln to work with local alignments

NEW FEATURES

  - added return.cds parameter to cds2aa for local alignments

                 Changes in version 1.7.4 (2024-03-18)                  

BUG FIXES

  - fixed pal2nal

                 Changes in version 1.7.3 (2024-03-14)                  

BUG FIXES

  - fixed dnastring2kaks to return correct orientation
  - fixed pal2nal to use gap_pos-n_i_codons_added-1

                 Changes in version 1.7.2 (2024-03-14)                  

BUG FIXES

  - fixed pal2nal to cover individual gaps longer than 1

                 Changes in version 1.7.1 (2024-03-13)                  

NEW FEATURES

  - added pal2nal
  - added cdsstring2codonaln
  - added indices2kaks
  - added KaKs Calculator 2.0 example to vignette

CHANGES

  - changed dnastring2kaks to use cdsstring2codonaln function

                 Changes in version 1.5.2 (2023-05-24)                  

NEW FEATURES

  - added aa2selfscore

                 Changes in version 1.5.1 (2023-05-22)                  

NEW FEATURES

  - additional option to use asymmetric score matrix (symmetric=FALSE)

CHANGES

  - changed rcpp_distSTRING.cpp
  - changed rcpp_pairwiseDeletionAA.cpp
  - changed rcpp_pairwiseDeletionDNA.cpp
  - changed aastring2dist.R
  - changed dnastring2dist.R

                 Changes in version 1.3.1 (2022-11-08)                  

NEW FEATURES

  - additional Genetic Codes into base.cpp

                 Changes in version 1.1.7 (2022-10-05)                  

CHANGES

  - changed licence into GPL-3 to account for KaKs Calculator 2.0
    licence

                 Changes in version 1.1.6 (2022-09-22)                  

CHANGES

  - changed test-rcpp_KaKs

                 Changes in version 1.1.5 (2022-09-19)                  

CHANGES

  - changed rcpp_KaKs data access from data.frame to list

                 Changes in version 1.1.4 (2022-07-16)                  

BUG FIXES

  - fixed rcpp Warnings

                 Changes in version 1.1.3 (2022-07-11)                  

BUG FIXES

  - fixed rcpp indentation Warnings

                 Changes in version 1.1.2 (2022-07-05)                  

NEW FEATURES

  - Added KaKs Calculator 2.0 models as rcpp implementation

BUG FIXES

  - fixed some typos

                 Changes in version 1.1.1 (2022-06-30)                  

NEW FEATURES

  - Added cds2codonaln

                 Changes in version 0.99.3 (2022-03-18)                 

BUG FIXES

  - Fix RcppThread::LdFlags warning

                 Changes in version 0.99.2 (2022-01-28)                 

NEW FEATURES

  - Added RcppThread::ProgressBar

                 Changes in version 0.99.1 (2022-01-27)                 

CHANGES

  - Changed version number into 0.99.2
  - Changed URL links in DESCRIPTION

                 Changes in version 0.99.0 (2021-12-22)                 

NEW FEATURES

  - Submitted to Bioconductor

CHANGES

  - Changed version number into 0.99.1
  - Changed name from distSTRING into MSA2dist