NEWS.md

In kullrich/MSA2dist: MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

MSA2dist 1.11.1 (2024-11-14)

BUG FIXES

• fixed pal2nal
• fixed aastring2aabin to return alignment

NEW FEATURES

• added globalDeletionAA

MSA2dist 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

MSA2dist 1.7.4 (2024-03-18)

BUG FIXES

• fixed pal2nal

MSA2dist 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

MSA2dist 1.7.2 (2024-03-14)

BUG FIXES

• fixed pal2nal to cover individual gaps longer than 1

MSA2dist 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

MSA2dist 1.5.2 (2023-05-24)

NEW FEATURES

• added aa2selfscore

MSA2dist 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

MSA2dist 1.3.1 (2022-11-08)

NEW FEATURES

• additional Genetic Codes into base.cpp

MSA2dist 1.1.7 (2022-10-05)

CHANGES

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

MSA2dist 1.1.6 (2022-09-22)

CHANGES

• changed test-rcpp_KaKs

MSA2dist 1.1.5 (2022-09-19)

CHANGES

• changed rcpp_KaKs data access from data.frame to list

MSA2dist 1.1.4 (2022-07-16)

BUG FIXES

• fixed rcpp Warnings

MSA2dist 1.1.3 (2022-07-11)

BUG FIXES

• fixed rcpp indentation Warnings

MSA2dist 1.1.2 (2022-07-05)

NEW FEATURES

• Added KaKs Calculator 2.0 models as rcpp implementation

BUG FIXES

• fixed some typos

MSA2dist 1.1.1 (2022-06-30)

NEW FEATURES

• Added cds2codonaln

MSA2dist 0.99.3 (2022-03-18)

BUG FIXES

• Fix RcppThread::LdFlags warning

MSA2dist 0.99.2 (2022-01-28)

NEW FEATURES

• Added RcppThread::ProgressBar

MSA2dist 0.99.1 (2022-01-27)

CHANGES

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

MSA2dist 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

kullrich/MSA2dist documentation built on Nov. 14, 2024, 5:39 p.m.