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